@article{parker_villafuerte_miller_huynh_chapman_hanafy_jackson iii_miller_kathariou_2024, title={Genomic Analysis Points to Multiple Genetic Mechanisms for Non-Transformable <i>Campylobacter jejuni</i> ST-50}, volume={12}, ISSN={["2076-2607"]}, DOI={10.3390/microorganisms12020327}, abstractNote={Campylobacter jejuni and Campylobacter coli are well known for their natural competence, i.e., their capacity for the uptake of naked DNA with subsequent transformation. This study identifies non-transformable C. jejuni and C. coli strains from domestic animals and employs genomic analysis to investigate the strain genotypes and their associated genetic mechanisms. The results reveal genetic associations leading to a non-transformable state, including functional DNase genes from bacteriophages and mutations within the cts-encoded DNA-uptake system, which impact the initial steps of the DNA uptake during natural transformation. Interestingly, all 38 tested C. jejuni ST-50 strains from the United States exhibit a high prevalence of non-transformability, and the strains harbor a variety of these genetic markers. This research emphasizes the role of these genetic markers in hindering the transfer of antimicrobial resistance (AMR) determinants, providing valuable insights into the genetic diversity of Campylobacter. As ST-50 is a major clone of C. jejuni globally, we additionally determined the prevalence of the genetic markers for non-transformability among C. jejuni ST-50 from different regions of the world, revealing distinct patterns of evolution and a strong selective pressure on the loss of competence in ST-50 strains, particularly in the agricultural environment in the United States. Our findings contribute to a comprehensive understanding of genetic exchange mechanisms within Campylobacter strains, and their implications for antimicrobial resistance dissemination and evolutionary pathways within specific lineages.}, number={2}, journal={MICROORGANISMS}, author={Parker, Craig T. and Villafuerte, David A. and Miller, William G. and Huynh, Steven and Chapman, Mary H. and Hanafy, Zahra and Jackson III, James H. and Miller, Morgan A. and Kathariou, Sophia}, year={2024}, month={Feb} }
 @article{kirchner_miller_osborne_badgley_neidermeyer_kathariou_2023, title={Campylobacter Colonization and Diversity in Young Turkeys in the Context of Gastrointestinal Distress and Antimicrobial Treatment}, volume={11}, ISSN={["2076-2607"]}, DOI={10.3390/microorganisms11020252}, abstractNote={Young turkeys are vulnerable to undifferentiated gastrointestinal distress, including “irritable and crabby syndrome” (ICS), which compromises flock performance and is typically treated with a combination of penicillin and gentamicin (P/G). However, the effects of ICS and P/G treatment on Campylobacter remain poorly understood. We investigated the impact of ICS and P/G treatment on Campylobacter levels and diversity in four flocks from three turkey farms. Cecum and jejunum samples were analyzed weekly from day of hatch to week 4–5. All four flocks became colonized with multidrug resistant (MDR) Campylobacter jejuni and C. coli by week 2–3, and two developed ICS. ICS and P/G treatment did not significantly impact total Campylobacter levels or strain genotypes but impacted species and antimicrobial resistance (AMR) profiles. One flock was raised under antibiotic-free (ABF) conditions while another flock at the same farm was raised conventionally. The ABF flock did not develop ICS while its counterpart did. However, Campylobacter strains, AMR profiles and sequence types were generally shared between these two flocks. Our findings suggest that ICS and P/G treatment impacted Campylobacter population dynamics in commercial young turkey flocks, and that ABF flocks may become readily colonized by MDR strains from non-ABF flocks at the same farm.}, number={2}, journal={MICROORGANISMS}, author={Kirchner, Margaret and Miller, William G. and Osborne, Jason A. and Badgley, Brian and Neidermeyer, Jeffrey and Kathariou, Sophia}, year={2023}, month={Feb} }
 @article{lee_parsons_chen_dungan_kathariou_2023, title={Contrasting Genetic Diversity of Listeria Pathogenicity Islands 3 and 4 Harbored by Nonpathogenic Listeria spp.}, ISSN={["1098-5336"]}, DOI={10.1128/aem.02097-22}, abstractNote={
            Listeria monocytogenes
            is a serious foodborne pathogen that can harbor the pathogenicity islands
            Listeria
            pathogenicity island 3 (LIPI-3) and LIPI-4. Intriguingly, these have also been reported in nonpathogenic
            L. innocua
            from food and farm environments, though limited information is available for strains from the natural environment.
          }, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Lee, Sangmi and Parsons, Cameron and Chen, Yi and Dungan, Robert S. S. and Kathariou, Sophia}, year={2023}, month={Feb} }
 @article{brown_chen_ivanova_leekitcharoenphon_parsons_niedermeyer_gould_strules_mesa-cruz_kelly_et al._2023, title={Draft Genome Sequences of 158 Listeria monocytogenes Strains Isolated from Black Bears (Ursus americanus) in the United States}, volume={12}, ISSN={2576-098X}, url={http://dx.doi.org/10.1128/mra.00248-23}, DOI={10.1128/mra.00248-23}, abstractNote={
            Listeria monocytogenes
            is responsible for severe foodborne disease and major economic losses, but its potential reservoirs in natural ecosystems remain poorly understood. Here, we report the draft genome sequences of 158
            L. monocytogenes
            strains isolated from black bears (
            Ursus americanus
            ) in the southeastern United States between 2014 and 2017.
          }, number={7}, journal={Microbiology Resource Announcements}, publisher={American Society for Microbiology}, author={Brown, Phillip and Chen, Yi and Ivanova, Mirena and Leekitcharoenphon, Pimlapas and Parsons, Cameron and Niedermeyer, Jeffrey and Gould, Nicholas and Strules, Jennifer and Mesa-Cruz, J. Bernardo and Kelly, Marcella J. and et al.}, editor={Rasko, DavidEditor}, year={2023}, month={Jul} }
 @article{brown_kanenaka_chen_ivanova_leekitcharoenphon_elhanafi_kathariou_2023, title={Draft Genome Sequences of Closely Related Listeria monocytogenes Lineage III Strains Isolated from a Food Processing Environment and a Case of Human Listeriosis}, volume={5}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/mra.00250-23}, DOI={10.1128/mra.00250-23}, abstractNote={
            Listeria monocytogenes
            lineage III is genetically highly diverse, and closely related lineage III strains from food facilities and human listeriosis have not been reported. Here, we report the genome sequences of three closely related lineage III strains from Hawaii, namely, one isolated from a human case and two isolated from a produce storage facility.
          }, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Brown, Phillip and Kanenaka, Rebecca and Chen, Yi and Ivanova, Mirena and Leekitcharoenphon, Pimlapas and Elhanafi, Driss and Kathariou, Sophia}, editor={Rasko, DavidEditor}, year={2023}, month={May} }
 @article{lee_tham_danielsson-tham_lopez-valladares_chen_brown_kathariou_2023, title={Draft Genome Sequences of Heavy Metal-Resistant Listeria monocytogenes Strains of Sequence Type 14 (Clonal Complex 14) from Human Listeriosis Cases in Sweden}, volume={7}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/mra.00406-23}, DOI={10.1128/mra.00406-23}, abstractNote={
            Listeria monocytogenes
            of clonal complex 14 (CC14) is a potentially hypervirulent clone of serotype 1/2a but remains poorly characterized. We report the genome sequences of five sequence type 14 (ST14) (CC14) strains from human listeriosis cases in Sweden, which harbor a chromosomal heavy metal resistance island that is generally uncommon in serotype 1/2a.
          }, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Lee, Sangmi and Tham, Wilhelm and Danielsson-Tham, Marie-Louise and Lopez-Valladares, Gloria and Chen, Yi and Brown, Phillip and Kathariou, Sophia}, editor={Dennehy, John J.Editor}, year={2023}, month={Jul} }
 @article{vishnivetskaya_niedermeyer_guttierrez-rodriguerz_baltzegar_parsons_kathariou_thrash_2023, title={Draft genome sequence of <i>Exiguobacterium</i> sp. from whole cantaloupe, with inhibition capacity against <i>Listeria monocytogenes</i>}, ISSN={["2576-098X"]}, DOI={10.1128/mra.00850-23}, abstractNote={ABSTRACT}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Vishnivetskaya, Tatiana A. and Niedermeyer, Jeffrey and Guttierrez-Rodriguerz, Eduardo and Baltzegar, David and Parsons, Cameron and Kathariou, Sophia and Thrash, J. Cameron}, year={2023}, month={Dec} }
 @article{lee_sadat_kucerova_kathariou_2023, title={Draft genome sequences of <i>Listeria monocytogenes</i> strains of sequence type 1733 which constituted a pseudo-outbreak due to contaminated blood agar media}, ISSN={["2576-098X"]}, DOI={10.1128/mra.00732-23}, abstractNote={ABSTRACT}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Lee, Sangmi and Sadat, Asmaa and Kucerova, Zuzana and Kathariou, Sophia}, year={2023}, month={Dec} }
 @article{brown_murray_galsworthy_ivanova_leekitcharoenphon_ward_kucerova_chen_elhanafi_siletzky_et al._2023, title={Draft genome sequences of a historical collection of Listeria monocytogenes from humans and other sources, 1926-1964}, volume={9}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/MRA.00625-23}, DOI={10.1128/MRA.00625-23}, abstractNote={ABSTRACT}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Brown, Phillip and Murray, Robert G. E. and Galsworthy, Sara and Ivanova, Mirena and Leekitcharoenphon, Pimlapas and Ward, Todd and Kucerova, Zuzana and Chen, Yi and Elhanafi, Driss and Siletzky, Robin and et al.}, editor={Dennehy, John J.Editor}, year={2023}, month={Sep} }
 @article{brown_lee_elhanafi_tham_danielsson-tham_lopez-valladares_chen_ivanova_leekitcharoenphon_kathariou_2023, title={Investigation of a Listeria monocytogenes Chromosomal Immigration Control Region Reveals Diverse Restriction Modification Systems with Complete Sequence Type Conservation}, volume={11}, ISSN={["2076-2607"]}, url={https://doi.org/10.3390/microorganisms11030699}, DOI={10.3390/microorganisms11030699}, abstractNote={Listeria monocytogenes is a Gram-positive pathogen responsible for the severe foodborne disease listeriosis. A chromosomal hotspot between lmo0301 and lmo0305 has been noted to harbor diverse restriction modification (RM) systems. Here, we analyzed 872 L. monocytogenes genomes to better understand the prevalence and types of RM systems in this region, designated the immigration control region (ICR). Type I, II, III and IV RM systems were found in 86.1% of strains inside the ICR and in 22.5% of strains flanking the ICR. ICR content was completely conserved within the same multilocus sequence typing-based sequence type (ST), but the same RM system could be identified in diverse STs. The intra-ST conservation of ICR content suggests that this region may drive the emergence of new STs and promote clone stability. Sau3AI-like, LmoJ2 and LmoJ3 type II RM systems as well as type I EcoKI-like, and type IV AspBHI-like and mcrB-like systems accounted for all RM systems in the ICR. A Sau3AI-like type II RM system with specificity for GATC was harbored in the ICR of many STs, including all strains of the ancient, ubiquitous ST1. The extreme paucity of GATC recognition sites in lytic phages may reflect ancient adaptation of these phages to preempt resistance associated with the widely distributed Sau3AI-like systems. These findings indicate that the ICR has a high propensity for RM systems which are intraclonaly conserved and may impact bacteriophage susceptibility as well as ST emergence and stability.}, number={3}, journal={MICROORGANISMS}, author={Brown, Phillip and Lee, Sangmi and Elhanafi, Driss and Tham, Wilhelm and Danielsson-Tham, Marie-Louise and Lopez-Valladares, Gloria and Chen, Yi and Ivanova, Mirena and Leekitcharoenphon, Pimlapas and Kathariou, Sophia}, year={2023}, month={Mar} }
 @article{shah_wang_kathariou_salvi_2023, title={Optimization of Plasma-activated Water and Validation of a Potential Surrogate for Salmonella for Future Egg Washing Processes}, volume={86}, ISSN={["1944-9097"]}, DOI={10.1016/j.jfp.2022.100029}, abstractNote={Plasma-activated water (PAW) is considered a novel sanitizer for the food industry due to the antimicrobial mechanisms exhibited by reactive oxygen and nitrogen species. The plasma operation parameters can affect the chemistry of PAW and can therefore influence its microbial inactivation efficacy. This study statistically optimized the operating conditions of PAW (activation time, distance from nozzle, and volume of water) using response surface methodology. Two optimized conditions of PAW were identified for the inactivation of planktonic cells of the avirulent strain of Salmonella Typhimurium MHM112 providing a minimum reduction of 6.3 log. All three operating parameters significantly affected the physicochemical characteristics (pH, ORP, EC, nitrite, and nitrate) and microbial inactivation efficacy of PAW. Mixing of small batches using the two optimized conditions to obtain larger volumes did not significantly change the microbial inactivation. However, there were significant reductions in nitrite and nitrate concentrations in PAW due to the mixing of batches while the pH and ORP values remained unaffected. The storage of large volumes of PAW for 25 min at 40–46°C, which is the commercial egg washing temperature in the United States, did not significantly impact S. Typhimurium MHM112 inactivation or the physicochemical characteristics of PAW. A validation study using a cocktail of six pathogenic strains of Salmonella revealed no significant differences in inactivation between the avirulent S. Typhimurium MHM112 and the pathogenic strains, suggesting that the avirulent S. Typhimurium MHM112 may serve as a surrogate for sanitation of S. enterica at the optimized conditions of PAW. The results obtained from this study are useful for our long-term goal of evaluating PAW efficacy in surface egg washing to inactivate Salmonella.}, number={1}, journal={JOURNAL OF FOOD PROTECTION}, author={Shah, Urvi and Wang, Qingyang and Kathariou, Sophia and Salvi, Deepti}, year={2023}, month={Jan} }
 @article{wang_kathariou_salvi_2023, title={Plasma-activated water for inactivation of <i>Salmonella Typhimurium</i> avirulent surrogate: Applications in produce and shell egg and understanding the modes of action}, volume={187}, ISSN={["1096-1127"]}, DOI={10.1016/j.lwt.2023.115331}, abstractNote={Plasma-activated water (PAW) is gaining interest as a novel sanitizer for foods. However, the sanitizing efficacy of PAW varies under different conditions, and its modes of action and impacts on food quality need further investigation for it to be applied in the food industry. This study evaluated the inactivation efficacy of PAW against a Salmonella Typhimurium avirulent surrogate, investigated the underlying mechanisms, and assessed the impacts of PAW on the safety and quality of cherry tomatoes and shell eggs. PAW was effective in inactivating S. Typhimurium in a planktonic state (1.5–5.8 log CFU reduction in 2–5 min) and on the food surface (>5 log CFU reduction in 5 min). PAW prepared with deionized water vs. tap water did not differ significantly in sanitizing efficacy. Various reactive oxygen and nitrogen species (RONS) contributed to the antimicrobial property of PAW, with nitric oxide playing the most significant role. The acidic nature of PAW might synergistically affect bacteria by disrupting cell membrane and enhancing RONS permeation. PAW did not modify the visual appearance and internal pH of the treated foods. This study demonstrates that PAW has the potential to be applied as a novel sanitizer for fresh produce and egg washing.}, journal={LWT-FOOD SCIENCE AND TECHNOLOGY}, author={Wang, Qingyang and Kathariou, Sophia and Salvi, Deepti}, year={2023}, month={Sep} }
 @article{brown_hernandez_parsons_chen_gould_deperno_niedermeyer_kathariou_2023, title={Tetracycline resistance in Listeria monocytogenes and L. innocua from wild black bears (Ursus americanus) in the United States is mediated by novel transposable elements}, volume={89}, ISSN={["1098-5336"]}, url={https://doi.org/10.1128/aem.01205-23}, DOI={10.1128/aem.01205-23}, abstractNote={ABSTRACT}, number={11}, journal={Environmental Microbiology}, author={Brown, Phillip and Hernandez, Kevin and Parsons, Cameron and Chen, Yi and Gould, Nicholas and DePerno, Christopher S. and Niedermeyer, Jeffrey and Kathariou, Sophia}, editor={Dozois, Charles M.Editor}, year={2023}, month={Nov} }
 @article{lu_marchant_thompson_melgarejo_ignatova_damaj_trejo_paramo_reed_breidt_et al._2022, title={Bacteriophages Isolated From Turkeys Infecting Diverse Salmonella Serovars}, volume={13}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2022.933751}, abstractNote={Salmonella is one of the leading causes of foodborne illnesses worldwide. The rapid emergence of multidrug-resistant Salmonella strains has increased global concern for salmonellosis. Recent studies have shown that bacteriophages (phages) are novel and the most promising antibacterial agents for biocontrol in foods because phages specifically kill target bacteria without affecting other bacteria, do not alter organoleptic properties or nutritional quality of foods, and are safe and environmentally friendly. Due to the vast variation in Salmonella serotypes, large numbers of different and highly virulent Salmonella phages with broad host ranges are needed. This study isolated 14 Salmonella phages from turkey fecal and cecal samples. Six phages (Φ205, Φ206, Φ207, ΦEnt, ΦMont, and Φ13314) were selected for characterization. These phages were from all three families in the Caudovirales order. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) revealed that each phage had a unique structural protein profile. Each phage had a distinct host range. Φ207 and ΦEnt are both siphophages. They shared eight hosts, including seven different Salmonella serovars and one Shigella sonnei strain. These two phages showed different restriction banding patterns generated through EcoRI or HindIII digestion, but shared three bands from EcoRI digestion. ΦEnt displayed the broadest and very unusual host range infecting 11 Salmonella strains from nine serovars and three Shigella strains from two species, and thus was further characterized. The one-step growth curve revealed that ΦEnt had a short latent period (10 min) and relatively large burst size (100 PFU/infected cell). ΦEnt and its host showed better thermal stabilities in tryptic soy broth than in saline at 63 or 72°C. In the model food system (cucumber juice or beef broth), ΦEnt infection [regardless of the multiplicity of infections (MOIs) of 1, 10, and 100] resulted in more than 5-log10 reduction in Salmonella concentration within 4 or 5 h. Such high lytic activity combined with its remarkably broad and unusual host range and good thermal stability suggested that ΦEnt is a novel Salmonella phage with great potential to be used as an effective biocontrol agent against diverse Salmonella serovars in foods.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Lu, Zhongjing and Marchant, John and Thompson, Samantha and Melgarejo, Henry and Ignatova, Dzhuliya and Damaj, Rana and Trejo, Hedy and Paramo, Rodrigo and Reed, Ashley and Breidt, Fred and et al.}, year={2022}, month={Jul} }
 @article{hanafy_osborne_miller_parker_olson_jackson_kathariou_2022, title={Differences in the Propensity of Different Antimicrobial Resistance Determinants to Be Disseminated via Transformation in Campylobacter jejuni and Campylobacter coli}, volume={10}, ISSN={["2076-2607"]}, DOI={10.3390/microorganisms10061194}, abstractNote={Campylobacter jejuni and Campylobacter coli are leading zoonotic foodborne pathogens, and the drugs of choice for human campylobacteriosis are macrolides (e.g., erythromycin) and fluoroquinolones. C. jejuni and C. coli are naturally competent for transformation via naked DNA uptake, but potential differences in transformation frequency (TF) for different antimicrobial resistance (AMR) markers remain poorly understood. We determined TFs for resistance to different antibiotics using as recipient a derivative of C. jejuni NCTC 11168 (strain SN:CM) with donor DNA from multidrug-resistant C. jejuni or C. coli. TF for nalidixic acid resistance ranked significantly highest (~1.4 × 10−3), followed by resistance to streptomycin and gentamicin. Tetracycline resistance via chromosomal tet(O) was less commonly transferred (~7.6 × 10−7), while transformation to erythromycin resistance was rare (≤4.7 × 10−8). We also determined TFs with the contemporary poultry-derived strains C. jejuni FSIS 11810577 and C. coli FSIS 1710488 as recipients. TFs to nalidixic acid and streptomycin resistance remained the highest (~7 × 10−4). However, TF for gentamicin resistance was remarkably low in certain recipient–donor combinations, while average TF for erythromycin resistance was noticeably higher (~3 × 10−6) than with SN:CM. Findings from this experimental model provide insights into factors that may impact transformation-mediated transfer of AMR leading to AMR dissemination in the agricultural ecosystem.}, number={6}, journal={MICROORGANISMS}, author={Hanafy, Zahra and Osborne, Jason A. and Miller, William G. and Parker, Craig T. and Olson, Jonathan W. and Jackson, James H. and Kathariou, Sophia}, year={2022}, month={Jun} }
 @article{fan_foster_zhao_mukherjee_shrestha_parsons_kathariou_2022, title={Genomic Analysis Reveals That Isolation Temperature on Selective Media Introduces Genetic Variation in Campylobacter jejuni from Bovine Feces}, volume={11}, ISSN={["2076-0817"]}, DOI={10.3390/pathogens11060678}, abstractNote={Campylobacter jejuni is commonly isolated on selective media following incubation at 37 °C or 42 °C, but the impact of these temperatures on genome variation remains unclear. Previously, Campylobacter selective enrichments from the feces of steers before and after ceftiofur treatment were plated on selective agar media and incubated at either 37 °C or 42 °C. Here, we analyzed the whole genome sequence of C. jejuni strains of the same multilocus sequence typing (MLST)-based sequence type (ST) and isolated from the same sample upon incubation at both temperatures. Four such strain pairs (one ST8221 and three ST8567) were analyzed using core genome and whole genome MLST (cgMLST, wgMLST). Among the 1970 wgMLST loci, 7–25 varied within each pair. In all but one of the pairs more (1.7–8.5 fold) new alleles were found at 42 °C. Most frameshift, nonsense, or start-loss mutations were also found at 42 °C. Variable loci CAMP0575, CAMP0912, and CAMP0913 in both STs may regularly respond to different temperatures. Furthermore, frameshifts in four variable loci in ST8567 occurred at multiple time points, suggesting a persistent impact of temperature. These findings suggest that the temperature of isolation may impact the sequence of several loci in C. jejuni from cattle.}, number={6}, journal={PATHOGENS}, author={Fan, Sicun and Foster, Derek and Zhao, Shaohua and Mukherjee, Sampa and Shrestha, Yesha and Parsons, Cameron and Kathariou, Sophia}, year={2022}, month={Jun} }
 @article{brown_kucerova_gorski_chen_ivanova_leekitcharoenphon_parsons_niedermeyer_jackson_kathariou_2022, title={Horizontal Gene Transfer and Loss of Serotype-Specific Genes in Listeria monocytogenes Can Lead to Incorrect Serotype Designations with a Commonly-Employed Molecular Serotyping Scheme}, volume={12}, ISSN={["2165-0497"]}, url={https://doi.org/10.1128/spectrum.02745-22}, DOI={10.1128/spectrum.02745-22}, abstractNote={
            Listeria monocytogenes
            is a foodborne pathogen responsible for severe illness (listeriosis), especially in pregnant women and their fetuses, immunocompromised individuals, and the elderly. Three serotypes, 1/2a, 1/2b, and 4b, account for most human listeriosis, with certain serotype 4b clonal complexes (CCs) overrepresented in human disease.
          }, journal={MICROBIOLOGY SPECTRUM}, author={Brown, Phillip and Kucerova, Zuzana and Gorski, Lisa and Chen, Yi and Ivanova, Mirena and Leekitcharoenphon, Pimlapas and Parsons, Cameron and Niedermeyer, Jeffrey and Jackson, James and Kathariou, Sophia}, editor={Chousalkar, KapilEditor}, year={2022}, month={Dec} }
 @article{jayeola_farber_kathariou_2022, title={Induction of the Viable-but-Nonculturable State in Salmonella Contaminating Dried Fruit}, volume={88}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01733-21}, abstractNote={
            Salmonella
            is a leading foodborne pathogen globally causing numerous outbreaks of foodborne illnesses and remains the leading contributor to deaths attributed to foodborne disease in the United States and other industrialized nations. Therefore, efficient detection methods for
            Salmonella
            contaminating food are critical for public health and food safety.
          }, number={2}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Jayeola, Victor and Farber, J. M. and Kathariou, S.}, year={2022}, month={Jan} }
 @article{dong_wang_rodriguez_tang_kathariou_sun_yang_2022, title={Photoactivated carbon dots inducing bacterial functional and molecular alterations}, ISSN={["2633-5409"]}, DOI={10.1039/d2ma00403h}, abstractNote={Carbon dots (CDots) coupled with visible light exposure were found highly effective in the inactivation of bacterial pathogens.}, journal={MATERIALS ADVANCES}, author={Dong, Xiuli and Wang, Ping and Rodriguez, Cristian E. and Tang, Yongan and Kathariou, Sophia and Sun, Ya-Ping and Yang, Liju}, year={2022}, month={Jun} }
 @article{burnett_kucerova_freeman_kathariou_chen_smikle_2022, title={Whole-Genome Sequencing Reveals Multiple Subpopulations of Dominant and Persistent Lineage I Isolates of Listeria monocytogenes in Two Meat Processing Facilities during 2011-2015}, volume={10}, ISSN={["2076-2607"]}, DOI={10.3390/microorganisms10051070}, abstractNote={Listeria monocytogenes is a foodborne pathogen with a highly clonal population structure comprising multiple phylogenetic sub-groups that can persist within food processing environments and contaminate food. The epidemiology of L. monocytogenes is well-described in some developed countries; however, little is known about the prevalence and population structure of this pathogen in food and food processing environments located in less developed regions. The aim of this study was to determine the genetic characteristics and clonal relatedness of L. monocytogenes that were isolated from two Jamaican meat processing facilities. Of the 37 isolates collected between 2011 and 2015, only a single lineage II isolate was recovered (serotype 1/2c), and the remaining were lineage I isolates representing serotypes 4b, 1/2b, 3b, and two untypeable isolates. Pulsed-field gel electrophoresis (PFGE) delineated isolates into seven pulsotypes, and whole-genome sequencing (WGS) categorized most isolates within one of three clonal complexes (CC): CC2 (N = 12), CC5 (N = 11), and CC288 (N = 11). Isolates representing CC1 (N = 2) and CC9 (N = 1) were also recovered. Virulence-associated genes such as inlA and the LIPI-3 cluster were detected in multiple isolates, along with the stress survival islet cluster-1 (SSI-1), and benzalkonium (bcrABC) and cadmium (cad1, cad2, cad4) resistance cassettes. Multiple isolates that belong to the same CC and matching PFGE patterns were isolated from food and the environment from both facilities across multiple years, suggesting the presence of persistent strains of L. monocytogenes, and/or constant re-entry of the pathogens into the facilities from common sources. These findings highlight the ability of lineage I isolates of L. monocytogenes to colonize, persist, and predominate within two meat-producing environments, and underscores the need for robust surveillance strategies to monitor and mitigate against these important foodborne pathogens.}, number={5}, journal={MICROORGANISMS}, author={Burnett, Elton and Kucerova, Zuzana and Freeman, Molly and Kathariou, Sophia and Chen, Jessica and Smikle, Monica}, year={2022}, month={May} }
 @article{gorski_walker_romanolo_kathariou_2021, title={Growth and Survival of Attached Listeria on Lettuce and Stainless Steel Varies by Strain and Surface Type}, volume={84}, ISSN={["1944-9097"]}, DOI={10.4315/JFP-20-434}, abstractNote={The foodborne pathogen Listeria monocytogenes lives as a saprophyte in nature and can adhere to and grows on surfaces as diverse as leaves, sediment, and stainless steel. To discern the mechanisms used by L. monocytogenes for attachment and growth on various surfaces, we studied interactions between the pathogen on lettuce and stainless steel. A panel of 24 strains (23 of Listeria monocytogenes and 1 L. innocua ) was screened for attachment and growth on lettuce at 4 o C and 25 o C and on stainless steel at 10 o C and 37 o C. Overnight growth of attached cells resulted in a 0 - 3 log increase on lettuce, depending on the strain and the temperature. Among the worst performing strains on lettuce were two from a large cantaloupe outbreak, indicating that factors important for interactions with cantaloupe may be different from those required on lettuce tissue. Strains that grew the best on lettuce belonged to serotypes 1/2a, 1/2b, and 4b and were from cheese, potatoes, and water/sediment near produce fields. Confocal microscopy of L. monocytogenes tagged with constitutively expressed green fluorescent protein indicated associations with the cut edges and veins of lettuce leaves. On stainless steel coupons, there was a 5 - 7 log increase at 10 o C after 7 d and a 4 - 7 log increase at 37 o C after 40 h. Statistically, surface growth on stainless steel was better for serotype 1/2a than for serotype 4b strains, even though certain serotype 4b strains grew well on the coupons. The latter included strains that originated from produce and water/sediment. Some strains were fit in both environments, while others showed variability between the two different surfaces. Further analysis of these strains should reveal molecular factors needed for adherence and surface growth of L. monocytogenes on different biotic and abiotic surfaces.}, number={5}, journal={JOURNAL OF FOOD PROTECTION}, author={Gorski, Lisa and Walker, Samarpita and Romanolo, Kelly F. and Kathariou, Sophia}, year={2021}, month={May}, pages={903–911} }
 @article{brown_chen_siletzky_parsons_jaykus_eifert_ryser_logue_stam_brown_et al._2021, title={Harnessing Whole Genome Sequence Data for Facility-Specific Signatures for Listeria monocytogenes: A Case Study With Turkey Processing Plants in the United States}, volume={5}, ISSN={["2571-581X"]}, url={http://dx.doi.org/10.3389/fsufs.2021.742353}, DOI={10.3389/fsufs.2021.742353}, abstractNote={Listeria monocytogenes is a Gram-positive foodborne pathogen responsible for the severe disease listeriosis and notorious for its ability to persist in food processing plants, leading to contamination of processed, ready-to-eat foods. L. monocytogenes persistence in various food processing environments (FPEs) has been extensively investigated by various subtyping tools, with increasing use of whole genome sequencing (WGS). However, major knowledge gaps remain. There is a need for facility-specific molecular signatures not only for adequate attribution of L. monocytogenes to a specific FPE but also for improved understanding of the ecology and evolution of L. monocytogenes in the food processing ecosystem. Furthermore, multiple strains can be recovered from a single FPE sample, but their diversity can be underestimated with common molecular subtyping tools. In this study we investigated a panel of 54 L. monocytogenes strains from four turkey processing plants in the United States. A combination of WGS and phenotypic assays was employed to assess strain persistence as well as identify facility-specific molecular signatures. Comparative analysis of allelic variation across the whole genome revealed that allelic profiles have the potential to be specific to individual processing plants. Certain allelic profiles remained associated with individual plants even when closely-related strains from other sources were included in the analysis. Furthermore, for certain sequence types (STs) based on the seven-locus multilocus sequence typing scheme, presence and location of premature stop codons in inlA, inlB length, prophage sequences, and the sequence content of a genomic hotspot could serve as plant-specific signatures. Interestingly, the analysis of different isolates from the same environmental sample revealed major differences not only in serotype and ST, but even in the sequence content of strains of the same ST. This study highlights the potential for WGS data to be deployed for identification of facility-specific signatures, thus facilitating the tracking of strain movement through the food chain. Furthermore, deployment of WGS for intra-sample strain analysis allows for a more complete environmental surveillance of L. monocytogenes in food processing facilities, reducing the risk of failing to detect strains that may be clinically relevant and potentially novel.}, journal={FRONTIERS IN SUSTAINABLE FOOD SYSTEMS}, publisher={Frontiers Media SA}, author={Brown, Phillip and Chen, Yi and Siletzky, Robin and Parsons, Cameron and Jaykus, Lee-Ann and Eifert, Joseph and Ryser, Elliot and Logue, Catherine M. and Stam, Christina and Brown, Eric and et al.}, editor={Brown, PhillipEditor}, year={2021}, month={Oct} }
 @article{lee_parsons_chen_hanafy_brown_kathariou_2021, title={Identification and Characterization of a Novel Genomic Island Harboring Cadmium and Arsenic Resistance Genes in Listeria welshimeri}, volume={11}, ISSN={["2218-273X"]}, DOI={10.3390/biom11040560}, abstractNote={Listeria monocytogenes, the bacterial foodborne pathogen responsible for the severe disease listeriosis, frequently exhibits heavy metal resistance. Concurrent resistance to cadmium and arsenic in L. monocytogenes is strongly associated with the 35-kb chromosomal island LGI2. LGI2 has been encountered repeatedly among L. monocytogenes serotype 4b hypervirulent clones but, surprisingly, not among non-pathogenic Listeria spp. Here we describe a novel LGI2 variant, LGI2-3, in two L. welshimeri strains from an urban aquatic environment. Whole genome sequence analysis revealed that the genomes were closely related except for one prophage region and confirmed a chromosomally integrated LGI2-3. It harbored a cystathionine beta-lyase gene previously only encountered in LGI2-1 of L. monocytogenes clonal complex 1 but was otherwise most closely related to LGI2. LGI2-3 harbored a novel cadAC cassette (cadA7C7) that, like LGI2′s cadA4C4, was associated with lower-level tolerance to cadmium (MIC 50 μg/mL) than other cadAC cassettes (MIC ≥ 140 μg/mL). CadA sequence analysis identified two amino acids that may be important for mediating different levels of cadmium tolerance. Our findings clearly demonstrated the potential for LGI2-like islands to be harbored by non-pathogenic Listeria spp. and generate intriguing hypotheses on the genetic diversity mediated by this island and its transfer among Listeria spp.}, number={4}, journal={BIOMOLECULES}, author={Lee, Sangmi and Parsons, Cameron and Chen, Yi and Hanafy, Zahra and Brown, Eric and Kathariou, Sophia}, year={2021}, month={Apr} }
 @article{fan_foster_miller_osborne_kathariou_2021, title={Impact of Ceftiofur Administration in Steers on the Prevalence and Antimicrobial Resistance of Campylobacter spp.}, volume={9}, ISSN={["2076-2607"]}, DOI={10.3390/microorganisms9020318}, abstractNote={Bacterial resistance to ceftiofur raises health concerns due to ceftiofur’s extensive veterinary usage and structural similarity with the human antibiotic ceftriaxone. Ceftiofur crystalline-free acid (CCFA) and ceftiofur hydrochloride (CHCL) are ceftiofur types used therapeutically in cattle, but their potential impacts on Campylobacter prevalence and antimicrobial resistance remain unclear. In this study two groups of steers were each treated with CCFA or CHCL. In vivo active drug concentrations were measured and fecal samples were analyzed for Campylobacter for up to 42 days post-treatment. Following administration, the colonic concentration of ceftiofur initially increased then dropped to pre-treatment levels by day 8. The estimated prevalence of Campylobacter spp. was significantly (p = 0.0009) higher during the first week after CCFA treatment than after CHCL treatment (81.3% vs. 45.2%). Campylobacter jejuni predominated overall, with other Campylobacter spp. mainly identified in the first week after CCFA treatment. No treatment impacts were noted on ceftiofur minimum inhibitory concentration (MIC) for C. jejuni (10–20 μg/mL). More C. jejuni genotypes were detected in CCFA-treated than CHCL-treated steers. These findings suggest that ceftiofur did not significantly impact Campylobacter prevalence or ceftiofur MIC. However, CHCL may be preferable due to the lower likelihood of temporary increases in Campylobacter prevalence.}, number={2}, journal={MICROORGANISMS}, author={Fan, Sicun and Foster, Derek and Miller, William G. and Osborne, Jason and Kathariou, Sophia}, year={2021}, month={Feb} }
 @article{harris_fidan_nelson_emanuel_jass_kathariou_niedermeyer_sharara_reyes_riveros-iregui_et al._2021, title={Microbial Contamination in Environmental Waters of Rural and Agriculturally-Dominated Landscapes Following Hurricane Florence}, volume={1}, ISSN={["2690-0637"]}, url={https://doi.org/10.1021/acsestwater.1c00103}, DOI={10.1021/acsestwater.1c00103}, abstractNote={Hurricane Florence brought unprecedented rainfall and flooding to Eastern North Carolina in 2018. Extensive flooding had the potential to mobilize microbial contaminants from a variety of sources. Our study evaluated microbial contaminants in surface waters at 40 sites across Eastern North Carolina 1 week after the hurricane made landfall (Phase 1) and one month later (Phase 2). High concentrations of Escherichia coli were detected in flowing channel and floodwater samples across both phases; however, channel samples during Phase 2 had higher concentrations of E. coli compared to Phase 1. Human- and swine-associated fecal markers were detected in 26% and 9% of samples, respectively, with no trends related to phase of sampling. Arcobacter butzleri was previously shown to be recovered from most (73%) samples, and detection of this pathogen was not associated with any source-associated fecal marker. Detection of Listeria spp. was associated with the swine-associated fecal marker. These results suggest that improved swine and human feces management should be explored to prevent microbial contamination in surface water, especially in regions where extreme rainfall may increase due to climate change. Sampling at higher frequency surrounding rainfall events would provide more detailed characterization of the risks posed by floodwater at different time scales and under different antecedent conditions.}, number={9}, journal={ACS ES&T WATER}, publisher={American Chemical Society (ACS)}, author={Harris, Angela R. and Fidan, Emine N. and Nelson, Natalie G. and Emanuel, Ryan E. and Jass, Theo and Kathariou, Sophia and Niedermeyer, Jeffrey and Sharara, Mahmoud and Reyes, Francis Lajara, III and Riveros-Iregui, Diego A. and et al.}, year={2021}, month={Sep}, pages={2012–2019} }
 @article{parsons_azizoglu_elhanafi_kathariou_2021, title={Mutant Construction and Integration Vector-Mediated Genetic Complementation in Listeria monocytogenes}, volume={2220}, ISBN={["978-1-0716-0981-1"]}, ISSN={["1940-6029"]}, DOI={10.1007/978-1-0716-0982-8_14}, abstractNote={Genes that play a role in stress response mechanisms and other phenotypes of Listeria monocytogenes can be identified by construction and screening of mutant libraries. In this chapter, we describe the construction and screening of mutant libraries of L. monocytogenes using the plasmid pMC38, carrying a mariner-based transposon system (TC1/mariner) and constructed by Cao et al. (Appl Environ Microbiol 73:2758–2761, 2007). Following screening of mutant libraries, putative mutants are identified and the transposon is localized, leading to identification of the genes responsible for the phenotype of interest. To confirm the role of the transposon-harboring gene in the relevant phenotype, transposon mutants are genetically complemented with the wild-type gene using the site-specific temperature-sensitive integration vector pPL2, constructed by Lauer et al. (J Bacteriol 184:4177–4186, 2002).}, journal={LISTERIA MONOCYTOGENES, 2 EDITION}, author={Parsons, Cameron and Azizoglu, Reha and Elhanafi, Driss and Kathariou, Sophia}, year={2021}, pages={177–185} }
 @article{guernier-cambert_trachsel_maki_qi_sylte_hanafy_kathariou_looft_2021, title={Natural Horizontal Gene Transfer of Antimicrobial Resistance Genes in Campylobacter spp. From Turkeys and Swine}, volume={12}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2021.732969}, abstractNote={Antibiotic-resistant Campylobacter constitutes a serious threat to public health. The clonal expansion of resistant strains and/or the horizontal spread of resistance genes to other strains and species can hinder the clinical effectiveness of antibiotics to treat severe campylobacteriosis. Still, gaps exist in our understanding of the risks of acquisition and spread of antibiotic resistance in Campylobacter. While the in vitro transfer of antimicrobial resistance genes between Campylobacter species via natural transformation has been extensively demonstrated, experimental studies have favored the use of naked DNA to obtain transformants. In this study, we used experimental designs closer to real-world conditions to evaluate the possible transfer of antimicrobial resistance genes between Campylobacter strains of the same or different species (Campylobacter coli or Campylobacter jejuni) and originating from different animal hosts (swine or turkeys). This was evaluated in vitro through co-culture experiments and in vivo with dual-strain inoculation of turkeys, followed by whole genome sequencing of parental and newly emerged strains. In vitro, we observed four independent horizontal gene transfer events leading to the acquisition of resistance to beta-lactams (blaOXA), aminoglycosides [aph(2′′)-If and rpsL] and tetracycline [tet(O)]. Observed events involved the displacement of resistance-associated genes by a mutated version, or the acquisition of genomic islands harboring a resistance determinant by homologous recombination; we did not detect the transfer of resistance-carrying plasmids even though they were present in some strains. In vivo, we recovered a newly emerged strain with dual-resistance pattern and identified the replacement of an existing non-functional tet(O) by a functional tet(O) in the recipient strain. Whole genome comparisons allowed characterization of the events involved in the horizontal spread of resistance genes between Campylobacter following in vitro co-culture and in vivo dual inoculation. Our study also highlights the potential for antimicrobial resistance transfer across Campylobacter species originating from turkeys and swine, which may have implications for farms hosting both species in close proximity.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Guernier-Cambert, Vanina and Trachsel, Julian and Maki, Joel and Qi, Jing and Sylte, Matthew J. and Hanafy, Zahra and Kathariou, Sophia and Looft, Torey}, year={2021}, month={Sep} }
 @article{dong_wang_darby_tang_overton_kathariou_sun_yang_2021, title={Photoactivated Carbon Dots for Inactivation of Foodborne Pathogens Listeria and Salmonella}, volume={87}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01042-21}, abstractNote={Foodborne infectious diseases have long been recognized as major challenges in public health. Contaminations of food processing facilities and equipment with foodborne pathogens occur often.}, number={23}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Dong, Xiuli and Wang, Ping and Darby, Jasmine P. and Tang, Yongan and Overton, Christopher M. and Kathariou, Sophia and Sun, Ya-Ping and Yang, Liju}, year={2021}, month={Dec} }
 @article{lopez-perez_sai_sakamachi_parsons_kathariou_ninomiya-tsuji_2021, title={TAK1 inhibition elicits mitochondrial ROS to block intracellular bacterial colonization}, volume={118}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.2023647118}, abstractNote={Significance}, number={25}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Lopez-Perez, Wilfred and Sai, Kazuhito and Sakamachi, Yosuke and Parsons, Cameron and Kathariou, Sophia and Ninomiya-Tsuji, Jun}, year={2021}, month={Jun} }
 @misc{parsons_brown_kathariou_2021, title={Use of Bacteriophage Amended with CRISPR-Cas Systems to Combat Antimicrobial Resistance in the Bacterial Foodborne Pathogen Listeria monocytogenes}, volume={10}, ISSN={["2079-6382"]}, url={http://dx.doi.org/10.3390/antibiotics10030308}, DOI={10.3390/antibiotics10030308}, abstractNote={Listeria monocytogenes is a bacterial foodborne pathogen and the causative agent of the disease listeriosis, which though uncommon can result in severe symptoms such as meningitis, septicemia, stillbirths, and abortions and has a high case fatality rate. This pathogen can infect humans and other animals, resulting in massive health and economic impacts in the United States and globally. Listeriosis is treated with antimicrobials, typically a combination of a beta-lactam and an aminoglycoside, and L. monocytogenes has remained largely susceptible to the drugs of choice. However, there are several reports of antimicrobial resistance (AMR) in both L. monocytogenes and other Listeria species. Given the dire health outcomes associated with listeriosis, the prospect of antimicrobial-resistant L. monocytogenes is highly problematic for human and animal health. Developing effective tools for the control and elimination of L. monocytogenes, including strains with antimicrobial resistance, is of the utmost importance to prevent further dissemination of AMR in this pathogen. One tool that has shown great promise in combating antibiotic-resistant pathogens is the use of bacteriophages (phages), which are natural bacterial predators and horizontal gene transfer agents. Although native phages can be effective at killing antibiotic-resistant pathogens, limited host ranges and evolved resistance to phages can compromise their use in the efforts to mitigate the global AMR challenge. However, recent advances can allow the use of CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) to selectively target pathogens and their AMR determinants. Employment of CRISPR-Cas systems for phage amendment can overcome previous limitations in using phages as biocontrol and allow for the effective control of L. monocytogenes and its AMR determinants.}, number={3}, journal={ANTIBIOTICS-BASEL}, publisher={MDPI AG}, author={Parsons, Cameron and Brown, Phillip and Kathariou, Sophia}, editor={Brown, PhillipEditor}, year={2021}, month={Mar} }
 @article{brown_chen_parsons_brown_loessner_shen_kathariou_2021, title={Whole Genome Sequence Analysis of Phage-Resistant Listeria monocytogenes Serotype 1/2a Strains from Turkey Processing Plants}, volume={10}, ISSN={["2076-0817"]}, url={http://dx.doi.org/10.3390/pathogens10020199}, DOI={10.3390/pathogens10020199}, abstractNote={Listeria monocytogenes is a Gram-positive bacterial pathogen and the causative agent of listeriosis, a severe foodborne infection. L. monocytogenes is notorious for its ability to persist in food processing environments (FPEs) via a variety of adaptive traits. Even though traits such as cold tolerance, biofilm formation and sanitizer resistance have been extensively investigated for their roles in persistence of L. monocytogenes in FPEs, much less is known about resistance to bacteriophages. Previous studies explored phage resistance mechanisms in laboratory-created mutants but it is imperative to investigate phage resistance that is naturally exhibited in FPE-derived strains. Here, we integrated the analysis of whole genome sequence data from a panel of serotype 1/2a strains of sequence types 321 and 391 from turkey processing plants, with the determination of cell surface substituents required for phage adsorption and phage infection assays with the four wide-host-range phages A511, P100, 20422-1 and 805405-1. Using a specific set of recombinant phage protein probes, we discovered that phage-resistant strains lacked one or both of the serogroup 1/2-specific wall teichoic acid carbohydrate decorations, N-acetylglucosamine and rhamnose. Furthermore, these phage-resistant strains harbored substitutions in lmo1080, lmo1081, and lmo2550, which mediate carbohydrate decoration of the wall teichoic acids.}, number={2}, journal={PATHOGENS}, publisher={MDPI AG}, author={Brown, Phillip and Chen, Yi and Parsons, Cameron and Brown, Eric and Loessner, Martin J. and Shen, Yang and Kathariou, Sophia}, editor={Brown, PhillipEditor}, year={2021}, month={Feb} }
 @misc{parsons_lee_kathariou_2020, title={Dissemination and conservation of cadmium and arsenic resistance determinants in Listeria and other Gram-positive bacteria}, volume={113}, ISSN={["1365-2958"]}, DOI={10.1111/mmi.14470}, abstractNote={Abstract}, number={3}, journal={MOLECULAR MICROBIOLOGY}, author={Parsons, Cameron and Lee, Sangmi and Kathariou, Sophia}, year={2020}, month={Mar}, pages={560–569} }
 @article{jayeola_mcclelland_porwollik_chu_farber_kathariou_2020, title={Identification of Novel Genes Mediating Survival ofSalmonellaon Low-Moisture Foods via Transposon Sequencing Analysis}, volume={11}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2020.00726}, abstractNote={Salmonella enterica is the leading foodborne pathogen associated with outbreaks involving low-moisture foods (LMFs). However, the genes involved in Salmonella’s long-term survival on LMFs remain poorly characterized. In this study, in-shell pistachios were inoculated with Tn5-based mutant libraries of S. Enteritidis P125109, S. Typhimurium 14028s, and S. Newport C4.2 at approximate 108 CFU/g and stored at 25°C. Transposon sequencing analysis (Tn-seq) was then employed to determine the relative abundance of each Tn5 insertion site immediately after inoculation (T0), after drying (T1), and at 120 days (T120). In S. Enteritidis, S. Typhimurium, and S. Newport mutant libraries, the relative abundance of 51, 80, and 101 Tn5 insertion sites, respectively, was significantly lower at T1 compared to T0, while in libraries of S. Enteritidis and S. Typhimurium the relative abundance of 42 and 68 Tn5 insertion sites, respectively, was significantly lower at T120 compared to T1. Tn5 insertion sites with reduced relative abundance in this competition assay were localized in DNA repair, lipopolysaccharide biosynthesis and stringent response genes. Twelve genes among those under strong negative selection in the competition assay were selected for further study. Whole gene deletion mutants in ten of these genes, sspA, barA, uvrB, damX, rfbD, uvrY, lrhA, yifE, rbsR, and ompR, were impaired for individual survival on pistachios. The findings highlight the value of combined mutagenesis and sequencing to identify novel genes important for the survival of Salmonella in low-moisture foods.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Jayeola, Victor and McClelland, Michael and Porwollik, Steffen and Chu, Weiping and Farber, Jeffrey and Kathariou, Sophia}, year={2020}, month={May} }
 @article{parsons_niedermeyer_gould_brown_strules_parsons_bernardo mesa‐cruz_kelly_hooker_chamberlain_et al._2020, title={Listeria monocytogenes
            at the human–wildlife interface: black bears (
            Ursus americanus
            ) as potential vehicles for
            Listeria}, volume={13}, ISBN={1751-7915}, ISSN={1751-7915 1751-7915}, url={http://dx.doi.org/10.1111/1751-7915.13509}, DOI={10.1111/1751-7915.13509}, abstractNote={Summary}, number={3}, journal={Microbial Biotechnology}, publisher={Wiley}, author={Parsons, Cameron and Niedermeyer, Jeff and Gould, Nicholas and Brown, Phillip and Strules, Jennifer and Parsons, Arielle W. and Bernardo Mesa‐Cruz, J. and Kelly, Marcella J. and Hooker, Michael J. and Chamberlain, Michael J. and et al.}, editor={Brown, PhillipEditor}, year={2020}, month={May}, pages={706–721} }
 @article{dong_ge_abu rabe_mohammed_wang_tang_kathariou_yang_sun_2020, title={Photoexcited state properties and antibacterial activities of carbon dots relevant to mechanistic features and implications}, volume={170}, ISSN={["1873-3891"]}, DOI={10.1016/j.carbon.2020.08.025}, abstractNote={Carbon dots (CDots) are strongly absorptive over the visible spectrum, with the effective photon-harvesting driving rich excited state processes and properties. In this work, spectroscopic probing of these processes and properties is coupled with the evaluation of the photoinduced bactericidal function of CDots, aimed toward making correlations among the findings from the former and those from the latter on the inactivation of bacterial pathogens. Within the general mechanistic framework for CDots, the observed effective and efficient antibacterial activities of the CDots under visible light are attributed to major contributions by the initially photo-generated electrons and holes that are trapped at passivated surface defect sites of the dots, in addition to the traditional reactive oxygen species (ROS) produced in the emissive excited states from the recombination of the redox pairs. Such major contributions to the inactivation of the bacteria by the separated redox species in CDots can not be quenched by ROS scavengers commonly used in the study of photodynamic effects with classical molecular photosensitizers, thus making light-activated CDots uniquely potent antimicrobial agents. The characteristic features of photoexcited CDots and their related mechanistic implications are discussed in reference to the similar behaviors and mechanistic model of conventional semiconductor quantum dots.}, journal={CARBON}, author={Dong, Xiuli and Ge, Lin and Abu Rabe, Dina I and Mohammed, Oluwayemisi O. and Wang, Ping and Tang, Yongan and Kathariou, Sophia and Yang, Liju and Sun, Ya-Ping}, year={2020}, month={Dec}, pages={137–145} }
 @article{foster_jacob_farmer_callahan_theriot_kathariou_cernicchiaro_prange_papich_2019, title={Ceftiofur formulation differentially affects the intestinal drug concentration, resistance of fecal Escherichia coli, and the microbiome of steers}, volume={14}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0223378}, abstractNote={Antimicrobial drug concentrations in the gastrointestinal tract likely drive antimicrobial resistance in enteric bacteria. Our objective was to determine the concentration of ceftiofur and its metabolites in the gastrointestinal tract of steers treated with ceftiofur crystalline-free acid (CCFA) or ceftiofur hydrochloride (CHCL), determine the effect of these drugs on the minimum inhibitory concentration (MIC) of fecal Escherichia coli, and evaluate shifts in the microbiome. Steers were administered either a single dose (6.6 mg/kg) of CCFA or 2.2 mg/kg of CHCL every 24 hours for 3 days. Ceftiofur and its metabolites were measured in the plasma, interstitium, ileum and colon. The concentration and MIC of fecal E. coli and the fecal microbiota composition were assessed after treatment. The maximum concentration of ceftiofur was higher in all sampled locations of steers treated with CHCL. Measurable drug persisted longer in the intestine of CCFA-treated steers. There was a significant decrease in E. coli concentration (P = 0.002) within 24 hours that persisted for 2 weeks after CCFA treatment. In CHCL-treated steers, the mean MIC of ceftiofur in E. coli peaked at 48 hours (mean MIC = 20.45 ug/ml, 95% CI = 10.29–40.63 ug/ml), and in CCFA-treated steers, mean MIC peaked at 96 hours (mean MIC = 10.68 ug/ml, 95% CI = 5.47–20.85 ug/ml). Shifts in the microbiome of steers in both groups were due to reductions in Firmicutes and increases in Bacteroidetes. CCFA leads to prolonged, low intestinal drug concentrations, and is associated with decreased E. coli concentration, an increased MIC of ceftiofur in E. coli at specific time points, and shifts in the fecal microbiota. CHCL led to higher intestinal drug concentrations over a shorter duration. Effects on E. coli concentration and the microbiome were smaller in this group, but the increase in the MIC of ceftiofur in fecal E. coli was similar.}, number={10}, journal={PLOS ONE}, author={Foster, Derek M. and Jacob, Megan E. and Farmer, Kyle A. and Callahan, Benjamin J. and Theriot, Casey M. and Kathariou, Sophia and Cernicchiaro, Natalia and Prange, Timo and Papich, Mark G.}, year={2019}, month={Oct} }
 @article{parsons_chen_niedermeyer_hernandez_kathariou_2019, title={Draft Genome Sequence of Multidrug-Resistant Listeria innocua Strain UAM003-1A, Isolated from a Wild Black Bear (Ursus americanus)}, volume={8}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.01281-19}, abstractNote={
            There is currently limited knowledge of the genome sequences of nonpathogenic
            Listeria
            species, especially strains from wildlife. Here, we report the draft genome sequence and associated genome information of an antibiotic-resistant
            Listeria innocua
            strain, UAM003-1A, isolated from the feces of a black bear in California, USA.
          }, number={47}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Parsons, Cameron and Chen, Yi and Niedermeyer, Jeffrey and Hernandez, Kevin and Kathariou, Sophia}, year={2019}, month={Nov} }
 @article{rahimi_kathariou_fletcher_grimes_2019, title={Effect of a direct-fed microbial and prebiotic on performance and intestinal histomorophology of turkey poults challenged with Salmonella and Campylobacter}, volume={98}, ISSN={["1525-3171"]}, DOI={10.3382/ps/pez436}, abstractNote={Salmonella and Campylobacter are leading human foodborne pathogens commonly associated with poultry and poultry products, and several methods to control these pathogens have been applied to poultry production. This study was conducted to evaluate the effect of CALSPORIN, (CSP), a direct-fed microbial (DFM), and yeast cell wall (Saccharomyces cervisiae, IMW50, a mannanoligosaccharide (MOS)-based prebiotic, on performance, levels of Salmonella and Campylobacter in the feces, and intestinal histomorphometry in turkey poults. A 21-day battery cage study was conducted using 4 dietary treatments, including: an unsupplemented basal diet (corn and soybean-based) as negative control (NC); basal diet supplemented with 0.05% DFM; basal diet supplemented with 0.05% MOS; and basal diet supplemented with 0.05% mixture of DFM and MOS at equal proportions. Female Large White turkey poults (n = 336) were randomly distributed in 6 electrically-heated battery cages with 4 treatments and 12 replicates per treatment (7 poults per replicate pen). The first 16 pens were not inoculated with bacteria, while poults in pens 17 to 32 were orally challenged at day 7 with 105 CFU Salmonella Heidelberg and the poults in pens 33 to 48 were orally challenged at day 7 with 105 CFU Campylobacter jejuni. Feed consumption, body weight, and feed conversion ratio were measured weekly and at the end of the experiment. At day 21, fresh fecal samples from each pen were collected for Salmonella and Campylobacter enumeration and ileal tissue samples were collected from 1 bird per pen for histomorphology examination. DFM and MOS supplementation was accompanied with reduced levels of Salmonella shed by the treated birds compared to the control group, and with increased body weight (P ≤ 0.05). The surface area of villi increased in the MOS-supplemented group compared to the control group (P ≤ 0.05). There was a significant difference in V:C ratio between supplemented groups and control group (P ≤ 0.05). Based on these results, there is potential for CALSPORIN and IMW50 to reduce Salmonella shedding in feces, enhance ileal mucosal health, and improve growth performance of turkey poults.}, number={12}, journal={POULTRY SCIENCE}, author={Rahimi, Shaban and Kathariou, Sophia and Fletcher, Oscar and Grimes, Jesse L.}, year={2019}, month={Dec}, pages={6572–6578} }
 @misc{parsons_lee_kathariou_2019, title={Heavy Metal Resistance Determinants of the Foodborne Pathogen Listeria monocytogenes}, volume={10}, ISSN={["2073-4425"]}, DOI={10.3390/genes10010011}, abstractNote={Listeria monocytogenes is ubiquitous in the environment and causes the disease listeriosis. Metal homeostasis is one of the key processes utilized by L. monocytogenes in its role as either a saprophyte or pathogen. In the environment, as well as within an animal host, L. monocytogenes needs to both acquire essential metals and mitigate toxic levels of metals. While the mechanisms associated with acquisition and detoxification of essential metals such as copper, iron, and zinc have been extensively studied and recently reviewed, a review of the mechanisms associated with non-essential heavy metals such as arsenic and cadmium is lacking. Resistance to both cadmium and arsenic is frequently encountered in L. monocytogenes, including isolates from human listeriosis. In addition, a growing body of work indicates the association of these determinants with other cellular functions such as virulence, suggesting the importance of further study in this area.}, number={1}, journal={GENES}, author={Parsons, Cameron and Lee, Sangmi and Kathariou, Sophia}, year={2019}, month={Jan} }
 @article{sai_parsons_house_kathariou_ninomiya-tsuji_2019, title={Necroptosis mediators RIPK3 and MLKL suppress intracellular Listeria replication independently of host cell killing}, volume={218}, ISSN={["1540-8140"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85067213651&partnerID=MN8TOARS}, DOI={10.1083/jcb.201810014}, abstractNote={RIPK3, a key mediator of necroptosis, has been implicated in the host defense against viral infection primary in immune cells. However, gene expression analysis revealed that RIPK3 is abundantly expressed not only in immune organs but also in the gastrointestinal tract, particularly in the small intestine. We found that orally inoculated Listeria monocytogenes, a bacterial foodborne pathogen, efficiently spread and caused systemic infection in Ripk3-deficient mice while almost no dissemination was observed in wild-type mice. Listeria infection activated the RIPK3-MLKL pathway in cultured cells, which resulted in suppression of intracellular replication of Listeria. Surprisingly, Listeria infection–induced phosphorylation of MLKL did not result in host cell killing. We found that MLKL directly binds to Listeria and inhibits their replication in the cytosol. Our findings have revealed a novel functional role of the RIPK3-MLKL pathway in nonimmune cell-derived host defense against Listeria invasion, which is mediated through cell death–independent mechanisms.}, number={6}, journal={JOURNAL OF CELL BIOLOGY}, publisher={Rockefeller University Press}, author={Sai, Kazuhito and Parsons, Cameron and House, John S. and Kathariou, Sophia and Ninomiya-Tsuji, Jun}, year={2019}, month={Jun}, pages={1994–2005} }
 @article{parsons_jahanafroozi_kathariou_2019, title={Requirement of lmo1930, a Gene in the Menaquinone Biosynthesis Operon, for Esculin Hydrolysis and Lithium Chloride Tolerance in Listeria monocytogenes}, volume={7}, ISSN={["2076-2607"]}, DOI={10.3390/microorganisms7110539}, abstractNote={Listeria monocytogenes is a foodborne pathogen that is widely distributed in nature, having been isolated from a variety of sources such as soil, water, plant matter, and animals. In addition, L. monocytogenes is often detected in the regular sampling of food and food processing environments. The most common method for detecting L. monocytogenes is the use of selective enrichments. Both lithium chloride and esculin, in combination with ferric ammonium citrate, are utilized in several of the most commonly-employed selective enrichment schemes for L. monocytogenes. Here we report that transposon-based inactivation of lmo1930, one of the genes in the menaquinone biosynthesis operon, via transposon mutagenesis severely impaired the ability of L. monocytogenes to grow in the presence of lithium chloride or hydrolyze esculin, and conferred reduced growth and colony size. All phenotypes were restored upon genetic complementation. Thus, strains of L. monocytogenes with mutations leading to inactivation of lmo1930 may evade many commonly-used selective enrichment protocols employed in the detection of L. monocytogenes.}, number={11}, journal={MICROORGANISMS}, author={Parsons, Cameron and Jahanafroozi, Midya and Kathariou, Sophia}, year={2019}, month={Nov} }
 @article{good_miller_niedermeyer_osborne_siletzky_carver_kathariou_2019, title={Strain-Specific Differences in Survival of Campylobacter spp. in Naturally Contaminated Turkey Feces and Water}, volume={85}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01579-19}, abstractNote={
            Campylobacter jejuni
            and
            Campylobacter coli
            are leading foodborne pathogens, with poultry as a major reservoir. Due to their growth requirements, these
            Campylobacter
            spp. may be unable to replicate once excreted by their avian hosts, but their survival in feces and the environment is critical for transmission in the farm ecosystem. Reducing the prevalence of
            Campylobacter
            -positive flocks can have major impacts in controlling both contamination of poultry products and environmental dissemination of the pathogens. However, understanding the capacity of these pathogens to survive in transmission-relevant vehicles such as feces and farmhouse water remains poorly understood, and little information is available on species- and strain-associated differences in survival. Here, we employed model conditions to investigate the survival of
            C. jejuni
            and
            C. coli
            from naturally colonized turkey flocks, and with diverse genotypes and antimicrobial resistance profiles, in turkey feces and in farmhouse water.
          }, number={22}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Good, Lesley and Miller, William G. and Niedermeyer, Jeffrey and Osborne, Jason and Siletzky, Robin M. and Carver, Donna and Kathariou, Sophia}, year={2019}, month={Nov} }
 @article{musser_berger_parsons_kathariou_johannes_2019, title={Vaccine strain Listeria monocytogenes abscess in a dog: a case report}, volume={15}, ISSN={["1746-6148"]}, DOI={10.1186/s12917-019-2216-y}, abstractNote={Abstract}, number={1}, journal={BMC VETERINARY RESEARCH}, author={Musser, Margaret L. and Berger, Erika P. and Parsons, Cameron and Kathariou, Sophia and Johannes, Chad M.}, year={2019}, month={Dec} }
 @article{jayeola_parsons_gorski_kathariou_2019, title={Validation of an ampicillin selection protocol to enrich for mutants of Listeria monocytogenes unable to replicate on fresh produce}, volume={366}, ISSN={["1574-6968"]}, DOI={10.1093/femsle/fnz076}, abstractNote={ABSTRACT}, number={7}, journal={FEMS MICROBIOLOGY LETTERS}, author={Jayeola, Victor and Parsons, C. and Gorski, L. and Kathariou, S.}, year={2019}, month={Apr} }
 @article{bolinger_zhang_miller_kathariou_2018, title={Lack of Evidence for erm(B) Infiltration Into Erythromycin-Resistant Campylobacter coli and Campylobacter jejuni from Commercial Turkey Production in Eastern North Carolina: A Major Turkey-Growing Region in the United States}, volume={15}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2018.2477}, abstractNote={In Campylobacter spp., resistance to erythromycin and other macrolides has typically implicated ribosomal mutations, especially substitutions in the 23S rRNA genes. However, in 2014, the macrolide resistance gene erm(B) was reported for the first time in Campylobacter and shown to be harbored by a multidrug resistance island in the chromosome of the swine-derived strain Campylobacter coli ZC113. erm(B)-positive C. coli and Campylobacter jejuni strains from the food supply have been mostly reported from China. However, erm(B)-positive C. coli isolates were also detected recently in fecal samples from turkeys in Spain. To determine whether erm(B) may be harbored by erythromycin-resistant Campylobacter from commercial turkey production in eastern North Carolina, a major turkey-growing region in the United States, we investigated a panel of 178 erythromycin-resistant isolates (174 C. coli, 4 C. jejuni) using PCR with erm(B)-specific primers. None of the isolates were PCR-positive for erm(B) and sequence analysis of a subset of these erythromycin-resistant isolates revealed that all harbored A2075G substitutions in the 23S rRNA genes. Data fail to provide evidence for infiltration of erm(B) into erythromycin-resistant Campylobacter from commercial turkey production in this region and suggest the need for continuing surveillance.}, number={11}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Bolinger, Hannah K. and Zhang, Qijing and Miller, William G. and Kathariou, Sophia}, year={2018}, month={Nov}, pages={698–700} }
 @article{lee_chen_gorski_ward_osborne_kathariou_2018, title={Listeria monocytogenes Source Distribution Analysis Indicates Regional Heterogeneity and Ecological Niche Preference among Serotype 4b Clones}, volume={9}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.00396-18}, abstractNote={ABSTRACT}, number={2}, journal={MBIO}, author={Lee, Sangmi and Chen, Yi and Gorski, Lisa and Ward, Todd J. and Osborne, Jason and Kathariou, Sophia}, year={2018} }
 @article{haddad_johnson_kathariou_metris_phister_pielaat_tassou_wells-bennikh_zwietering_2018, title={Next generation microbiological risk assessment-Potential of omics data for hazard characterisation}, volume={287}, ISSN={["1879-3460"]}, DOI={10.1016/j.ijfoodmicro.2018.04.015}, abstractNote={According to the World Health Organization estimates in 2015, 600 million people fall ill every year from contaminated food and 420,000 die. Microbial risk assessment (MRA) was developed as a tool to reduce and prevent risks presented by pathogens and/or their toxins. MRA is organized in four steps to analyse information and assist in both designing appropriate control options and implementation of regulatory decisions and programs. Among the four steps, hazard characterisation is performed to establish the probability and severity of a disease outcome, which is determined as function of the dose of toxin and/or pathogen ingested. This dose-response relationship is subject to both variability and uncertainty. The purpose of this review/opinion article is to discuss how Next Generation Omics can impact hazard characterisation and, more precisely, how it can improve our understanding of variability and limit the uncertainty in the dose-response relation. The expansion of omics tools (e.g. genomics, transcriptomics, proteomics and metabolomics) allows for a better understanding of pathogenicity mechanisms and virulence levels of bacterial strains. Detection and identification of virulence genes, comparative genomics, analyses of mRNA and protein levels and the development of biomarkers can help in building a mechanistic dose-response model to predict disease severity. In this respect, systems biology can help to identify critical system characteristics that confer virulence and explain variability between strains. Despite challenges in the integration of omics into risk assessment, some omics methods have already been used by regulatory agencies for hazard identification. Standardized methods, reproducibility and datasets obtained from realistic conditions remain a challenge, and are needed to improve accuracy of hazard characterisation. When these improvements are realized, they will allow the health authorities and government policy makers to prioritize hazards more accurately and thus refine surveillance programs with the collaboration of all stakeholders of the food chain.}, journal={INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY}, author={Haddad, Nabila and Johnson, Nick and Kathariou, Sophia and Metris, Aline and Phister, Trevor and Pielaat, Annemarie and Tassou, Chrysoula and Wells-Bennikh, Marjon H. J. and Zwietering, Marcel H.}, year={2018}, month={Dec}, pages={28–39} }
 @article{rantsiou_kathariou_winkler_skandamis_saint-cyr_rouzeau-szynalski_amezquita_2018, title={Next generation microbiological risk assessment: opportunities of whole genome sequencing (WGS) for foodborne pathogen surveillance, source tracking and risk assessment}, volume={287}, ISSN={["1879-3460"]}, DOI={10.1016/j.ijfoodmicro.2017.11.007}, abstractNote={Whole genome sequencing (WGS) of important foodborne pathogens is a technology under development, but is already employed in routine surveillance by public health agencies and is being increasingly exploited in tracing transmission routes and identifying contamination events (source tracking) that take place in the farm-to-fork continuum. Furthermore, data generated from WGS, complemented by other –omics data, have the potential to be integrated into and strengthen microbiological risk assessment. In this paper, we discuss the contribution of WGS in diverse areas important to food safety and public health. Additionally, an outlook of future WGS applications, which should contribute to our understanding of the ecology and physiology of foodborne microorganisms, is presented.}, journal={INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY}, author={Rantsiou, Kalliopi and Kathariou, Sophia and Winkler, Annet and Skandamis, Panos and Saint-Cyr, Manuel Jimmy and Rouzeau-Szynalski, Katia and Amezquita, Alejandro}, year={2018}, month={Dec}, pages={3–9} }
 @article{niedermeyer_ring_miller_genger_lindsey_osborne_kathariou_2018, title={Proximity to Other Commercial Turkey Farms Affects Colonization Onset, Genotypes, and Antimicrobial Resistance Profiles of Campylobacter spp. in Turkeys: Suggestive Evidence from a Paired-Farm Model}, volume={84}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01212-18}, abstractNote={
            Colonization of poultry with
            Campylobacter
            at the farm level is complex, poorly understood, and critically linked to contamination of poultry products, which is known to constitute a leading risk factor for human campylobacteriosis. Here, we investigated the use of a paired-farm design under standard production conditions and in the absence of experimental inoculations to assess potential impacts of farm and host genetics on prevalence, antimicrobial resistance and genotypes of
            Campylobacter
            in commercial turkeys of two different breeds. Data suggest impacts of farm proximity to other commercial turkey farms on the onset of colonization, genotypes, and antimicrobial resistance profiles of
            Campylobacter
            colonizing the birds. Furthermore, the significant association of a specific multidrug-resistant
            Campylobacter jejuni
            strain with turkeys of one breed suggests colonization partnerships at the
            Campylobacter
            strain-turkey breed level. The study design avoids potential pitfalls associated with experimental inoculations, providing novel insights into the dynamics of turkey colonization with
            Campylobacter
            in actual farm ecosystems.
          }, number={18}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Niedermeyer, Jeffrey A. and Ring, Lynde and Miller, William G. and Genger, Seiche and Lindsey, Christina Parr and Osborne, Jason and Kathariou, Sophia}, year={2018}, month={Sep} }
 @article{price_parsons_kathariou_2018, title={RNA Helicase Mediates Competitive Fitness of Listeria monocytogenes on the Surface of Cantaloupe}, volume={4}, ISSN={["2311-7524"]}, DOI={10.3390/horticulturae4040040}, abstractNote={Listeria monocytogenes is a foodborne pathogen that is implicated in numerous outbreaks of disease (listeriosis) via fresh produce. The genetic features of L. monocytogenes that allow adherence and growth on produce remain largely uncharacterized. In this study, two non-motile transposon mutants were characterized for attachment, growth, and survival on the surface of cantaloupe rind. One of the mutants, L1E4, harbored a single transposon insertion in a DEAD-box RNA helicase gene (lmo0866 homolog), while the other, M1A5, harbored an insertion in a gene from a flagellum biosynthesis and chemotaxis gene cluster (lmo0694 homolog). When inoculated alone, neither mutant was significantly impaired in growth or survival on the surface of cantaloupe at either 25 or 37 °C. However, when co-inoculated with the wildtype parental strain, the RNA helicase mutant L1E4 had a clear competitive disadvantage, while the relative fitness of M1A5 was not noticeably impacted. Genetic complementation of L1E4 with the intact RNA helicase gene restored relative fitness on cantaloupe. The findings suggest that the DEAD-box RNA helicase encoded by the lmo0866 homolog is critical for relative fitness of L. monocytogenes on cantaloupe. Mutant L1E4 was pleiotropic, being not only non-motile but also cold-sensitive and with reduced hemolytic activity, warranting further studies to elucidate the role of this helicase in the competitive fitness of L. monocytogenes on produce.}, number={4}, journal={HORTICULTURAE}, author={Price, Robert and Parsons, Cameron and Kathariou, Sophia}, year={2018}, month={Dec} }
 @article{wolfe_wiepz_schotzko_bondarenko_durning_simmons_mejia_faith_sampene_suresh_et al._2017, title={Acute Fetal Demise with First Trimester Maternal Infection Resulting from Listeria monocytogenes in a Nonhuman Primate Model}, volume={8}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.01938-16}, abstractNote={ABSTRACT}, number={1}, journal={MBIO}, author={Wolfe, Bryce and Wiepz, Gregory J. and Schotzko, Michele and Bondarenko, Gennadiy I. and Durning, Maureen and Simmons, Heather A. and Mejia, Andres and Faith, Nancy G. and Sampene, Emmanuel and Suresh, Marulasiddappa and et al.}, year={2017} }
 @article{gkana_giaouris_doulgeraki_kathariou_nychas_2017, title={Biofilm formation by Salmonella Typhimurium and Staphylococcus aureus on stainless steel under either mono- or dual-species multi-strain conditions and resistance of sessile communities to sub-lethal chemical disinfection}, volume={73}, ISSN={["1873-7129"]}, DOI={10.1016/j.foodcont.2016.09.038}, abstractNote={Intercellular interactions encountered within and between different bacterial species are believed to play key roles in both biofilm formation and antimicrobial resistance. In this study, Salmonella Typhimurium and Staphylococcus aureus (3 strains per species) were left to form biofilms on stainless steel coupons incubated at 20 °C for 144 h (i.e. 6 days), in periodically renewable growth medium, under either mono- or dual-species conditions. Subsequently, the developed sessile communities were exposed for 6 min to sub-lethal concentrations of: (i) benzalkonium chloride (BC, 50 ppm), (ii) sodium hypochlorite (NaClO, 10 ppm), or (iii) peroxyacetic acid (PAA, 10 ppm). The dominance of each strain in the mono- and dual-species biofilm communities, both before and after disinfection, was monitored by pulsed field gel electrophoresis (PFGE). Results revealed that dual-species conditions led to a significant (ca. 10-fold) reduction in the number of sessile cells for both species, compared to mono-species ones, with interspecies interactions however found to not exert any significant effect on the disinfection resistance of each species as a whole. However, PFGE analysis revealed that the different strains here employed behaved differently with regard to biofilm formation and disinfection resistance, with this effect to be also strongly dependent on the culture conditions (mono-/dual-species) and the disinfectant applied. Such results expand our knowledge on multi-species biofilms formed by foodborne pathogenic bacteria and could hopefully be helpful in our efforts to develop effective elimination strategies and thus improve food safety.}, journal={FOOD CONTROL}, author={Gkana, Eleni N. and Giaouris, Efstathios D. and Doulgeraki, Agapi I. and Kathariou, Sophia and Nychas, George-John E.}, year={2017}, month={Mar}, pages={838–846} }
 @article{dutta_altermann_crespo_olson_siletzky_kathariou_2017, title={Identification of a Campylobacter coli methyltransferase targeting adenines at GATC sites}, volume={364}, DOI={10.1093/femsle/fnw268}, abstractNote={Abstract Campylobacter coli can infect humans and colonize multiple other animals, but its host‐associated genes or adaptations are poorly understood. Adenine methylation at GATC sites, resulting in MboI resistance of genomic DNA, was earlier frequently detected among C. coli from swine but not among turkey‐derived isolates. The underlying genetic basis has remained unknown. Comparative genome sequence analyses of C. coli 6461, a swine‐derived strain with MboI‐resistant DNA, revealed two chromosomal ORFs, 0059 and 0060, encoding a putative DNA methyltransferase and a conserved hypothetical protein, respectively, which were lacking from the genome of the turkey‐derived C. coli strain 11601, which had MboI‐susceptible DNA. To determine whether ORF0059 mediated MboI resistance and hence encoded a putative N6‐adenine DNA methyltransferase, the gene was cloned immediately upstream of a chloramphenicol resistance cassette (cat) and a PCR fragment harboring ORF0059‐cat was transformed into C. coli 11601. The transformants had MboI‐resistant DNA, suggesting a direct role of this gene in methylation of adenines at GATC sites. In silico analyses suggested that the ORF0059‐ORF0060 cassette was more frequent among C. coli from swine than certain other sources (e.g. cattle, humans). Potential impacts of ORF0059‐mediated methylation on C. coli host preference and other adaptations remain to be elucidated.}, number={7}, journal={FEMS Microbiology Letters}, author={Dutta, V. and Altermann, E. and Crespo, M. D. and Olson, J. W. and Siletzky, R. M. and Kathariou, S.}, year={2017} }
 @article{parsons_lee_jayeola_kathariou_2017, title={Novel Cadmium Resistance Determinant in Listeria monocytogenes}, volume={83}, ISSN={["1098-5336"]}, DOI={10.1128/aem.02580-16}, abstractNote={ABSTRACT}, number={5}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Parsons, Cameron and Lee, Sangmi and Jayeola, Victor and Kathariou, Sophia}, year={2017}, month={Mar} }
 @article{parsons_costolo_brown_kathariou_2017, title={Penicillin-binding protein encoded by pbp4 is involved in mediating copper stress in Listeria monocytogenes}, volume={364}, ISSN={["1574-6968"]}, url={http://dx.doi.org/10.1093/femsle/fnx207}, DOI={10.1093/femsle/fnx207}, abstractNote={ABSTRACT Listeria monocytogenes raises major food safety and public health concerns due to its potential for severe foodborne disease and persistent colonization of food processing facilities. Copper is often employed to control pathogens in agriculture and is increasingly used in healthcare facilities, but mechanisms mediating tolerance of L. monocytogenes to copper remain poorly understood. A mariner‐based mutant library of L. monocytogenes 2011L‐2858, implicated in the 2011 listeriosis outbreak via whole cantaloupe, was screened for growth at sublethal levels of copper yielding mutant G2B4 with decreased copper tolerance. The transposon was localized in pbp4 (lmo2229 homolog), encoding a penicillin‐binding protein (PBP). In addition to reduced copper tolerance, G2B4 exhibited increased susceptibility to &bgr;‐lactam antibiotics, reduced biofilm formation and reduced virulence in the Galleria mellonella model. Mutant phenotypes were fully restored upon genetic complementation of G2B4 with intact pbp4. Findings provide the first evidence for the role of a PBP in copper tolerance of L. monocytogenes and suggest that pbp4 may be a suitable target to enable the use of lower levels of copper or enhance the effectiveness of levels currently in use. Given the wide distribution of PBPs and their highly conserved nature, this could have profound impacts in regard to ecology and control of L. monocytogenes and other microorganisms.}, number={20}, journal={FEMS MICROBIOLOGY LETTERS}, publisher={Oxford University Press (OUP)}, author={Parsons, Cameron and Costolo, Ben and Brown, Phillip and Kathariou, Sophia}, editor={Brown, PhillipEditor}, year={2017}, month={Oct} }
 @article{lee_ward_jima_parsons_kathariou_2017, title={The Arsenic Resistance-Associated Listeria Genomic Island LGI2 Exhibits Sequence and Integration Site Diversity and a Propensity for Three Listeria monocytogenes Clones with Enhanced Virulence}, volume={83}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01189-17}, abstractNote={ABSTRACT}, number={21}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Lee, Sangmi and Ward, Todd J. and Jima, Dereje D. and Parsons, Cameron and Kathariou, Sophia}, year={2017}, month={Nov} }
 @misc{bolinger_kathariou_2017, title={The Current State of Macrolide Resistance in Campylobacter spp.: Trends and Impacts of Resistance Mechanisms}, volume={83}, ISSN={["1098-5336"]}, DOI={10.1128/aem.00416-17}, abstractNote={ABSTRACT}, number={12}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Bolinger, Hannah and Kathariou, Sophia}, year={2017}, month={Jun} }
 @misc{garner_kathariou_2016, title={Fresh Produce-Associated Listeriosis Outbreaks, Sources of Concern, Teachable Moments, and Insights}, volume={79}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028x.jfp-15-387}, abstractNote={Foodborne transmission of Listeria monocytogenes was first demonstrated through the investigation of the 1981 Maritime Provinces outbreak involving coleslaw. In the following two decades, most listeriosis outbreaks involved foods of animal origin, e.g., deli meats, hot dogs, and soft cheeses. L. monocytogenes serotype 4b, especially epidemic clones I, II, and Ia, were frequently implicated in these outbreaks. However, since 2008 several outbreaks have been linked to diverse types of fresh produce: sprouts, celery, cantaloupe, stone fruit, and apples. The 2011 cantaloupe-associated outbreak was one of the deadliest foodborne outbreaks in recent U.S. history. This review discusses produce-related outbreaks of listeriosis with a focus on special trends, unusual findings, and potential paradigm shifts. With the exception of sprouts, implicated produce types were novel, and outbreaks were one-time events. Several involved serotype 1/2a, and in the 2011 cantaloupe-associated outbreak, serotype 1/2b was for the first time conclusively linked to a common-source outbreak of invasive listeriosis. Also in this outbreak, for the first time multiple strains were implicated in a common-source outbreak. In 2014, deployment of whole genome sequencing as part of outbreak investigation validated this technique as a pivotal tool for outbreak detection and speedy resolution. In spite of the unusual attributes of produce-related outbreaks, in all but one of the investigated cases (the possible exception being the coleslaw outbreak) contamination was traced to the same sources as those for outbreaks associated with other vehicles (e.g., deli meats), i.e., the processing environment and equipment. The public health impact of farm-level contamination remains uncharacterized. This review highlights knowledge gaps regarding virulence and other potentially unique attributes of produce outbreak strains, the potential for novel fresh produce items to become unexpectedly implicated in outbreaks, and the key role of good control strategies in the processing environment.}, number={2}, journal={JOURNAL OF FOOD PROTECTION}, author={Garner, Danisha and Kathariou, Sophia}, year={2016}, month={Feb}, pages={337–344} }
 @article{palerme_pan_parsons_kathariou_ward_jacob_2016, title={Isolation and characterization of atypical Listeria monocytogenes associated with a canine urinary tract infection}, volume={28}, ISSN={1040-6387 1943-4936}, url={http://dx.doi.org/10.1177/1040638716661381}, DOI={10.1177/1040638716661381}, abstractNote={Listeria monocytogenes, a well-described cause of encephalitis and abortion in ruminants and of food-borne illness in humans, is rarely associated with disease in companion animals. A case of urinary tract infection associated with an atypical, weakly hemolytic L. monocytogenes strain is described in a diabetic dog. The serotype of the L. monocytogenes isolate was determined to be 1/2a (3a), with the multilocus genotyping pattern 2.72_1/2a. A nucleotide substitution (Gly145Asp) was detected at residue 145 in the promoter prfA region. This residue is within the critical helix-turn-helix motif of PrfA. The source of the L. monocytogenes strain remains unknown, and the dog recovered after a 4-week course of cephalexin (30 mg/kg orally twice daily).}, number={5}, journal={Journal of Veterinary Diagnostic Investigation}, publisher={SAGE Publications}, author={Palerme, Jean-Sébastien and Pan, Po Ching and Parsons, Cameron T. and Kathariou, Sophia and Ward, Todd J. and Jacob, Megan E.}, year={2016}, month={Aug}, pages={604–607} }
 @article{pritchard_jacob_ward_parsons_kathariou_wood_2016, title={Listeria monocytogenes septicemia in an immunocompromised dog}, volume={45}, ISSN={["1939-165X"]}, DOI={10.1111/vcp.12363}, abstractNote={Abstract}, number={2}, journal={VETERINARY CLINICAL PATHOLOGY}, author={Pritchard, Jessica C. and Jacob, Megan E. and Ward, Todd J. and Parsons, Cameron T. and Kathariou, Sophia and Wood, Michael W.}, year={2016}, month={Jun}, pages={254–259} }
 @article{crespo_altermann_olson_miller_chandrashekhar_kathariou_2016, title={Novel plasmid conferring kanamycin and tetracycline resistance in the turkey-derived Campylobacter jejuni strain 11601MD}, volume={86}, ISSN={["1095-9890"]}, DOI={10.1016/j.plasmid.2016.06.001}, abstractNote={In Campylobacter spp., resistance to the antimicrobials kanamycin and tetracycline is frequently associated with plasmid-borne genes. However, relatively few plasmids of Campylobacter jejuni have been fully characterized to date. A novel plasmid (p11601MD; 44,095 nt) harboring tet(O) was identified in C. jejuni strain 11601MD, which was isolated from the jejunum of a turkey produced conventionally in North Carolina. Analysis of the p11601MD sequence revealed the presence of a high-GC content cassette with four genes that included tet(O) and a putative aminoglycoside transferase gene (aphA-3) highly similar to kanamycin resistance determinants. Several genes putatively involved in conjugative transfer were also identified on the plasmid. These findings will contribute to a better understanding of the distribution of potentially self-mobilizing plasmids harboring antibiotic resistance determinants in Campylobacter spp. from turkeys and other sources.}, journal={PLASMID}, author={Crespo, M. D. and Altermann, E. and Olson, J. and Miller, W. G. and Chandrashekhar, K. and Kathariou, S.}, year={2016}, month={Jul}, pages={32–37} }
 @article{crespo_kathariou_grimes_cox_buhr_frye_miller_jackson_smith_2016, title={Routes of transmission of Salmonella and Campylobacter in breeder turkeys}, volume={25}, ISSN={["1537-0437"]}, DOI={10.3382/japr/pfw035}, abstractNote={Abstract Salmonella and Campylobacter are frequent colonizers of the intestinal tracts of poultry and have often been associated with human foodborne illness. The entry, transmission, and prevalence of both pathogens have been extensively studied in chickens but little information is available for turkeys. This project monitored turkey breeder hens and toms from d of hatch to 65 wk of age with the objective of determining routes of transmission for Salmonella and Campylobacter throughout the turkey production cycle. Breeder poults were separated by sex and then into 2 groups (control and inoculated) for each sex. The inoculated group was orally gavaged with marker strains of both Salmonella and Campylobacter. The inoculated groups (toms and hens) were placed on the opposite side of a growout house from the uninoculated groups. Fecal samples, intestinal samples and organs, feed, drinkers, and potential vectors such as insects and mice, were analyzed at different times until 65 wk. Monitoring showed that Campylobacter spread rapidly and cross-contaminated turkeys throughout the growout house. For both Salmonella and Campylobacter, naturally occurring strains that were first isolated in control groups at wk 3 and 4, respectively, outcompeted marker strains several wk post inoculation and persisted in the flock. The most common naturally occurring strains were C. jejuni (tetracycline resistant), C. coli (kanamycin resistant), and S. Agona. Campylobacter and Salmonella also were isolated from flies and from a mouse, confirming the importance of proper pest control and biosecurity to reduce the spread of the bacteria.}, number={4}, journal={JOURNAL OF APPLIED POULTRY RESEARCH}, author={Crespo, M. D. and Kathariou, S. and Grimes, J. L. and Cox, N. A. and Buhr, R. J. and Frye, J. G. and Miller, W. G. and Jackson, C. R. and Smith, D. P.}, year={2016}, month={Dec}, pages={591–609} }
 @article{ebrahimi_rahimi_khaki_grimes_kathariou_2016, title={The effects of probiotics, organic acid, and a medicinal plant on the immune system and gastrointestinal microflora in broilers challenged with Campylobacter jejuni}, volume={40}, ISSN={["1300-0128"]}, DOI={10.3906/vet-1502-68}, abstractNote={Campylobacter jejuni, a zoonotic bacterial pathogen with worldwide distribution, infects about 400 million humans in the world annually. In order to reduce C. Jejuni colonization in the gastrointestinal tracts of broilers and make chickens less susceptible to colonization, four commercial products based on organic acid, probiotics, and medicinal plants were used. In this experiment, 210 one-day-old male broiler chicks (Ross 308) were assigned to 7 treatment groups randomly with 3 replications and 10 birds in each pen. Birds were challenged on day 21 by 1 mL of 6 × 107 CFU/mL C. Jejuni live suspension and samples were collected on days 28 and 42. The immune system's efficiency was evaluated by lymphoid organ development assessment and two specific and nonspecific immune system tests. The cecal contents and liver were considered for C. Jejuni enumeration. According to the results, all treatments except one showed a significant difference from the control in terms of cecal colonization (P ≤ 0.001). Probiotic and Echinacea purpurea treatments could significantly increase the immune system's efficiency (P ≤ 0.001). In general, in this study we provide evidence that some commercial feed and water additives can reduce chickens' susceptibility to C. Jejuni colonization and also can effectively increase immune system efficiency.}, number={3}, journal={TURKISH JOURNAL OF VETERINARY & ANIMAL SCIENCES}, author={Ebrahimi, Hossein and Rahimi, Shaban and Khaki, Pejvak and Grimes, Jesse L. and Kathariou, Sophia}, year={2016}, pages={329–336} }
 @book{dna methods in food safety: molecular typing of foodborne and waterborne bacterial pathogens_2014, ISBN={["978-1-118-27867-3"]}, DOI={10.1002/9781118278666}, journal={DNA METHODS IN FOOD SAFETY: MOLECULAR TYPING OF FOODBORNE AND WATERBORNE BACTERIAL PATHOGENS}, year={2014}, pages={1–392} }
 @article{dutta_elhanafi_osborne_martinez_kathariou_2014, title={Genetic Characterization of Plasmid-Associated Triphenylmethane Reductase in Listeria monocytogenes}, volume={80}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01398-14}, abstractNote={ABSTRACT}, number={17}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Dutta, Vikrant and Elhanafi, Driss and Osborne, Jason and Martinez, Mira Rakic and Kathariou, Sophia}, year={2014}, month={Sep}, pages={5379–5385} }
 @article{lee_ward_graves_tarr_siletzky_kathariou_2014, title={Population Structure of Listeria monocytogenes Serotype 4b Isolates from Sporadic Human Listeriosis Cases in the United States from 2003 to 2008}, volume={80}, ISSN={["1098-5336"]}, DOI={10.1128/aem.00454-14}, abstractNote={ABSTRACT}, number={12}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Lee, Sangmi and Ward, Todd J. and Graves, Lewis M. and Tarr, Cheryl L. and Siletzky, Robin M. and Kathariou, Sophia}, year={2014}, month={Jun}, pages={3632–3644} }
 @article{artymovich_kim_linz_hall_kelley_kalbach_kathariou_gaymer_paschke_2013, title={A "successful allele" at Campylobacter jejuni contingency locus Cj0170 regulates motility; "successful alleles" at locus Cj0045 are strongly associated with mouse colonization}, volume={34}, ISSN={["1095-9998"]}, DOI={10.1016/j.fm.2013.01.007}, abstractNote={Campylobacter jejuni is an important foodborne pathogen of humans and its primary reservoir is the gastrointestinal (GI) tract of chickens. Our previous studies demonstrated that phase variation to specific “successful alleles” at C. jejuni contingency loci Cj0045 (successful alleles carry 9G or 10G homopolymeric tracts) and Cj0170 (successful allele carries a 10G homopolymeric tract) in C. jejuni populations is strongly associated with colonization and enteritis in C57BL/6 IL-10 deficient mice. In the current study, we strengthened the association between locus Cj0170, Cj0045, and mouse colonization. We generated 8 independent strains derived from C. jejuni 11168 strain KanR4 that carried a Cj0170 gene disruption and these were all non motile. Two randomly chosen strains with the Cj0170 gene disruption (DM0170-2 and DM0170-6) were gavaged into mice. DM0170-2 and DM0170-6 failed to colonize mice while the control strain that carried a “successful” Cj0170 10G allele was motile and did colonize mice. In parallel studies, when we inoculated C. jejuni strain 33292 into mice, the “unsuccessful” Cj0045 11G allele experienced phase variation to “successful” 9G and 10G alleles in 2 independent experiments prior to d4 post inoculation in mice while the “successful” 9G allele in the control strain remained stable through d21 post inoculation or shifted to other successful alleles. These data confirm that locus Cj0170 regulates motility in C. jejuni strain KanR4 and is a virulence factor in the mouse model. The data also support a possible role of locus Cj0045 as a virulence factor in strain 33292 in infection of mice.}, number={2}, journal={FOOD MICROBIOLOGY}, author={Artymovich, Katherine and Kim, Joo-Sung and Linz, John E. and Hall, David F. and Kelley, Lauren E. and Kalbach, Harrison L. and Kathariou, Sophia and Gaymer, Jean and Paschke, Brenda}, year={2013}, month={Jun}, pages={425–430} }
 @article{dutta_elhanafi_kathariou_2013, title={Conservation and Distribution of the Benzalkonium Chloride Resistance Cassette bcrABC in Listeria monocytogenes}, volume={79}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01751-13}, abstractNote={ABSTRACT}, number={19}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Dutta, Vikrant and Elhanafi, Driss and Kathariou, Sophia}, year={2013}, month={Oct}, pages={6067–6074} }
 @article{lee_rakic-martinez_graves_ward_siletzky_kathariou_2013, title={Genetic Determinants for Cadmium and Arsenic Resistance among Listeria monocytogenes Serotype 4b Isolates from Sporadic Human Listeriosis Patients}, volume={79}, ISSN={["1098-5336"]}, DOI={10.1128/aem.03551-12}, abstractNote={ABSTRACT}, number={7}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Lee, Sangmi and Rakic-Martinez, M. and Graves, L. M. and Ward, T. J. and Siletzky, R. M. and Kathariou, S.}, year={2013}, month={Apr}, pages={2471–2476} }
 @article{wassinger_zhang_tracy_munson_kathariou_wang_2013, title={Role of a GntR-Family Response Regulator LbrA in Listeria monocytogenes Biofilm Formation}, volume={8}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0070448}, abstractNote={The formation of Listeria monocytogenes biofilms contributes to persistent contamination in food processing facilities. A microarray comparison of L. monocytogenes between the transcriptome of the strong biofilm forming strain (Bfms) Scott A and the weak biofilm forming (Bfmw) strain F2365 was conducted to identify genes potentially involved in biofilm formation. Among 951 genes with significant difference in expression between the two strains, a GntR-family response regulator encoding gene (LMOf2365_0414), designated lbrA, was found to be highly expressed in Scott A relative to F2365. A Scott A lbrA-deletion mutant, designated AW3, formed biofilm to a much lesser extent as compared to the parent strain by a rapid attachment assay and scanning electron microscopy. Complementation with lbrA from Scott A restored the Bfms phenotype in the AW3 derivative. A second microarray assessment using the lbrA deletion mutant AW3 and the wild type Scott A revealed a total of 304 genes with expression significantly different between the two strains, indicating the potential regulatory role of LbrA in L. monocytogenes. A cloned copy of Scott A lbrA was unable to confer enhanced biofilm forming potential in F2365, suggesting that additional factors contributed to weak biofilm formation by F2365.}, number={7}, journal={PLOS ONE}, author={Wassinger, Andrew and Zhang, Lu and Tracy, Erin and Munson, Robert S., Jr. and Kathariou, Sophia and Wang, Hua H.}, year={2013}, month={Jul} }
 @misc{brul_bassett_cook_kathariou_mcclure_jasti_betts_2012, title={'Omics' technologies in quantitative microbial risk assessment}, volume={27}, DOI={10.1016/j.tifs.2012.04.004}, abstractNote={‘Omics’ tools are being developed at an ever increasing pace. Collectively, genome sequencing, genome-wide transcriptional analysis (transcriptomics), proteomics, metabolomics, flux analysis (‘fluxomics’) and other applications are captured under the term omics. The data generated using these tools allow researchers to gain an increasingly detailed insight into cellular responses to changes in the environment. For the area of microbiological food safety, these developments mean that mechanistic explanations of the response of microorganisms to food preservation treatments and environmental conditions in the food chain become more attainable. Importantly, the data need to be relevant to real conditions in foods and related environments. Currently, it is still often the case that these data are generated in pure cultures and under very specific conditions albeit that recent years have seen some true in situ analyses. The opportunities offered by the latter in analysing virulence as well as challenges faced in terms of experimental design (including the consideration of strain variability) in efforts to link omics data to phenotypic response and data integration for quantitative microbiological risk assessment in foods are discussed in the current paper. The paper is guided by the output of a workshop organized in May 2011 by the International Life Sciences Institute Europe (ILSI Europe) in which representatives from governmental bodies, industry and academia came together to discuss such challenges and consider how these may be met. In addition, the ILSI Europe workshop identified knowledge gaps where new omics studies can make major contributions.}, number={1}, journal={Trends in Food Science & Technology}, author={Brul, S. and Bassett, J. and Cook, P. and Kathariou, S. and McClure, P. and Jasti, P. R. and Betts, R.}, year={2012}, pages={12–24} }
 @article{crespo_olson_altermann_siletzky_kathariou_2012, title={Chromosomal tet(O)-Harboring Regions in Campylobacter coli Isolates from Turkeys and Swine}, volume={78}, ISSN={["0099-2240"]}, DOI={10.1128/aem.02258-12}, abstractNote={ABSTRACT}, number={23}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Crespo, M. D. and Olson, J. W. and Altermann, E. and Siletzky, R. M. and Kathariou, S.}, year={2012}, month={Dec}, pages={8488–8491} }
 @article{katharios-lanwermeyer_rakic-martinez_elhanafi_ratani_tiedje_kathariou_2012, title={Coselection of Cadmium and Benzalkonium Chloride Resistance in Conjugative Transfers from Nonpathogenic Listeria spp. to Other Listeriae}, volume={78}, ISSN={["0099-2240"]}, DOI={10.1128/aem.02245-12}, abstractNote={ABSTRACT}, number={21}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Katharios-Lanwermeyer, S. and Rakic-Martinez, M. and Elhanafi, D. and Ratani, S. and Tiedje, J. M. and Kathariou, S.}, year={2012}, month={Nov}, pages={7549–7556} }
 @article{ratani_siletzky_dutta_yildirim_osborne_lin_hitchins_ward_kathariou_2012, title={Heavy Metal and Disinfectant Resistance of Listeria monocytogenes from Foods and Food Processing Plants}, volume={78}, ISSN={["0099-2240"]}, DOI={10.1128/aem.01553-12}, abstractNote={ABSTRACT}, number={19}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Ratani, Shakir S. and Siletzky, Robin M. and Dutta, Vikrant and Yildirim, Suleyman and Osborne, Jason A. and Lin, Wen and Hitchins, Anthony D. and Ward, Todd J. and Kathariou, Sophia}, year={2012}, month={Oct}, pages={6938–6945} }
 @article{thanissery_kathariou_siletzky_smith_2012, title={Microbiology of prechill carcasses from medium- and fast-growing pastured broiler chicken strains}, volume={21}, ISSN={["1056-6171"]}, DOI={10.3382/japr.2012-00548}, abstractNote={SUMMARY Consumer demand is increasing for free-range and organic poultry products. The USDA requires that postchill broilers be tested for Escherichia coli, Salmonella, and Campylobacter. Microbiological data are limited on the fast-growing Cornish cross (CX) chickens or the medium-growing Freedom Rangers (FR), 2 predominant strains of pastured broilers grown in the Southeast region of the United States. The objective of the present study was to compare the levels of total coliforms and E. coli, as well as the prevalence of Campylobacter and Salmonella, in pastured CX and FR strains. In each of 2 trials, 40 CX and 40 FR broilers were raised together on pasture with water and supplemental feed. At market weight, birds were processed and 20 prechill carcasses of each strain were evaluated for enumeration of total coliforms and E. coli, as well as the prevalence of Salmonella. Cecal contents were direct plated for Campylobacter detection. Mean counts for total coliforms and E. coli (expressed in log cfu/mL) were 3.8 and 3.4 for FR, which was significantly lower (P < 0.05) than the 4.1 and 3.7 for the CX group. The Salmonella prevalence on carcasses was not different in trial 1 because of strain, but the FR strain had significantly lower Salmonella than the CX strain (50 vs. 100%, respectively) in trial 2. Irrespective of strain, the prevalence of Campylobacter was high (95% for FR vs. 100% for CX). In trial 2, although the medium-growing FR showed lower levels of total coliforms and E. coli, as well as a lower prevalence of Salmonella, even when reared with fast-growing CX, it is not known whether this could have been due to an inherent ability of FR to resist colonization or the benefit from longer residence on pasture.}, number={3}, journal={JOURNAL OF APPLIED POULTRY RESEARCH}, author={Thanissery, R. and Kathariou, S. and Siletzky, R. M. and Smith, D. P.}, year={2012}, month={Sep}, pages={623–629} }
 @article{faith_kim_azizoglu_kathariou_czuprynski_2012, title={Purine Biosynthesis Mutants (purA and purB) of Serotype 4b Listeria monocytogenes Are Severely Attenuated for Systemic Infection in Intragastrically Inoculated A/J Mice}, volume={9}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2011.1013}, abstractNote={In this study, we demonstrate that purA and purB transposon mutants of serotype 4b Listeria monocytogenes were severely impaired in their ability to colonize the gastrointestinal tract and cause systemic infection of the spleen, liver, and gallbladder following intragastric inoculation of A/J mice. The mutant strains were also impaired in their ability to multiply within Caco-2 human intestinal epithelial cells. Neither mutant was affected in resistance to synthetic gastric fluid (pH 4.5). These findings indicate that purine biosynthesis is critical for gastrointestinal virulence of L. monocytogenes serotype 4b in mice.}, number={5}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Faith, Nancy G. and Kim, Jae-Won and Azizoglu, Reha and Kathariou, Sophia and Czuprynski, Charles}, year={2012}, month={May}, pages={480–486} }
 @article{lee_ward_siletzky_kathariou_2012, title={Two Novel Type II Restriction-Modification Systems Occupying Genomically Equivalent Locations on the Chromosomes of Listeria monocytogenes Strains}, volume={78}, ISSN={["0099-2240"]}, DOI={10.1128/aem.07203-11}, abstractNote={ABSTRACT}, number={8}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Lee, Sangmi and Ward, T. J. and Siletzky, R. M. and Kathariou, S.}, year={2012}, month={Apr}, pages={2623–2630} }
 @article{vishnivetskaya_lucas_copeland_lapidus_rio_dalin_tice_bruce_goodwin_pitluck_et al._2011, title={Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp AT1b}, volume={193}, ISSN={["0021-9193"]}, DOI={10.1128/jb.00303-11}, abstractNote={ABSTRACT}, number={11}, journal={JOURNAL OF BACTERIOLOGY}, author={Vishnivetskaya, Tatiana A. and Lucas, Susan and Copeland, Alex and Lapidus, Alla and Rio, Tijana Glavina and Dalin, E. and Tice, Hope and Bruce, David C. and Goodwin, Lynne A. and Pitluck, Sam and et al.}, year={2011}, month={Jun}, pages={2880–2881} }
 @article{rahimi_kathariou_grimes_siletzky_2011, title={Effect of direct-fed microbials on performance and Clostridium perfringens colonization of turkey poults}, volume={90}, ISSN={["1525-3171"]}, DOI={10.3382/ps.2011-01342}, abstractNote={Clostridium perfringens is recognized as an enteric pathogen in humans, domestic animals, and livestock. This organism is associated with necrotic enteritis, gangrenous dermatitis, clostridial dermatitis (turkeys), and gizzard erosions in poultry. This study was conducted to evaluate the effectiveness of a direct-fed microbial (DFM), Primalac (Star Labs, Clarksdale, MO), in preventing intestinal colonization of turkey poults with C. perfringens. One-day-old turkey poults (n = 128) were randomly divided into 4 treatments with 4 replicates (8 birds/pen). Treatments were as follows: 1) basal diet without DFM (C); 2) basal diet supplemented with Primalac (1.5 kg/ton; PM); 3) basal diet with poults gavaged with C. perfringens (CCP); and 4) basal diet supplemented with Primalac and poults gavaged with C. perfringens (PMCP). Feed and water were provided ad libitum throughout the trials, and birds were inoculated with C. perfringens (10(8)cfu/mL) on d 3 and 7. On d 21, 2 birds/pen were killed, spleen and bursa of Fabricius were collected and weighed, and cecal contents were used for C. perfringens enumeration. Feed consumption, BW, and feed conversion were calculated throughout the trial (weekly and cumulatively). Data were analyzed using GLM of SAS (SAS Institute, Cary, NC; P < 0.05). Among the inoculated groups, birds fed the DFM-supplemented diet had significantly lower cecal C. perfringens counts than the birds fed the diet without the DFM. The C. perfringens (log(10) cfu/g) in ceca were as follows: C, 5.88; CCP, 7.26; PM, 5.35; PMCP, 6.19 ± 0.36. No differences were observed for BW (814 ± 11 g), feed conversion (1.33 ± 0.03), organ weights, or relative organ weights. Further studies are needed to fully ascertain the potential of using DFM to reduce the numbers of C. perfringens in the gastrointestinal tract of turkey poults.}, number={11}, journal={POULTRY SCIENCE}, author={Rahimi, S. and Kathariou, S. and Grimes, J. L. and Siletzky, R. M.}, year={2011}, month={Nov}, pages={2656–2662} }
 @book{pina fratamico_kathariou_2011, title={Genomes of foodborne and waterborne pathogens}, DOI={10.1128/9781555816902}, abstractNote={Table of Contents 1. Insights from Genomic Studies of the Foodborne and Waterborne Pathogen Escherichia coli O157:H7 Victor P. J. Gannon, Chad R. Laing, and Yongxiang Zhang 2. Shigella Genomes: a Tale of Convergent Evolution and Specialization through IS Expansion and Genome Reduction Jian Yang, Vartul Sangal, Qi Jin, and Jun Yu 3. Genome Rearrangements in Salmonella T. David Matthews and Stanley Maloy 4. Campylobacter and Arcobacter William G. Miller and Craig T. Parker 5. Comparative Genomics of Vibrio vulnificus: Biology and Applications Lien-I Hor, Hung-Yu Shu, Keh-Ming Wu, and Shih-Feng Tsai 6. Vibrio parahaemolyticus Kaori Izutsu and Tetsuya Iida 7. How Genomics Has Shaped Our Understanding of the Evolution and Emergence of Pathogenic Vibrio cholerae Salvador Almagro-Moreno, Ronan A. Murphy, and E. Fidelma Boyd 8. Genomics of the Enteropathogenic Yersiniae Alan McNally, Nicholas R. Thomson, and Brendan W. Wren 9. Staphylococcus aureus Scott Weese, Jinzhe Mao, and David M. Donovan 10. Genomics of Listeria monocytogenes and Other Members of the Genus Listeria Carmen Buchrieser and Philippe Glaser 11. Bacillus cereus Monika Ehling-Schulz, Rickard Knutsson, and Siegfried Scherer 12. Bacillus anthracis Jean F. Challacombe, Richard T. Okinaka, A. Christine Munk, Thomas S. Brettin, and Paul Keim 13. Clostridium botulinum Holger Bruggemann, Antje Woltherr, Christelle Mazuet, and Michel R. Popoff 14. Clostridium perfringens Karl A. Hassan and Ian T. Paulsen 15. Mycobacterium avium Subspecies paratuberculosis John P. Bannantine, Yung-Fu Chang, and Vivek Kapur 16. Foodborne Noroviruses David H. Kingsley 17. Hepatitis A and E Viruses Albert Bosch and Rosa M. Pinto 18. Genomics of Aspergillus flavus Mycotoxin Production Gary A. Payne, D. Ryan Georgianna, Jiujiang Yu, Ken Ehrlich, Greg OBrian, and Deepak Bhatnagar 19. Cryptosporidium spp. Guan Zhu and Lihua Xiao 20. Giardia lamblia: Molecular Studies of an Early-Branching Eukaryote Mark C. Jenkins and Katarzyna Miska 21. Cyclospora cayetanensis: a Review of the Genome Joan M. Shields 22. Impact of the Toxoplasma gondii Genome Project Benjamin M. Rosenthal 23. Genomic and Postgenomic Approaches To Understand the Pathogenesis of the Enteric Protozoan Parasite Entamoeba histolytica Kumiko Nakada-Tsukui and Tomoyoshi Nozaki}, publisher={Washington, DC: ASM Press}, author={Pina Fratamico, Yanhong Liu and Kathariou, Sophia}, year={2011} }
 @article{rakic-martinez_drevets_dutta_katic_kathariou_2011, title={Listeria monocytogenes Strains Selected on Ciprofloxacin or the Disinfectant Benzalkonium Chloride Exhibit Reduced Susceptibility to Ciprofloxacin, Gentamicin, Benzalkonium Chloride, and Other Toxic Compounds}, volume={77}, ISSN={["1098-5336"]}, DOI={10.1128/aem.05941-11}, abstractNote={ABSTRACT}, number={24}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Rakic-Martinez, Mira and Drevets, Douglas A. and Dutta, Vikrant and Katic, Vera and Kathariou, Sophia}, year={2011}, month={Dec}, pages={8714–8721} }
 @article{verghese_lok_wen_alessandria_chen_kathariou_knabel_2011, title={comK Prophage Junction Fragments as Markers for Listeria monocytogenes Genotypes Unique to Individual Meat and Poultry Processing Plants and a Model for Rapid Niche-Specific Adaptation, Biofilm Formation, and Persistence (vol 77, pg 3279, 2011)}, volume={77}, ISSN={["0099-2240"]}, DOI={10.1128/aem.05513-11}, abstractNote={Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania 16802; Department of Exploitation and Protection of Agricultural and Forest Resources, Agricultural Microbiology and Food Technology Sector, Faculty of Agriculture, University of Turin, Turin, Italy; Microbial Methods Development Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20740; and Department of Food Science, North Carolina State University, Raleigh, North Carolina 27695}, number={14}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Verghese, Bindhu and Lok, Mei and Wen, Jia and Alessandria, Valentina and Chen, Yi and Kathariou, Sophia and Knabel, Stephen}, year={2011}, month={Jul}, pages={5064–5064} }
 @article{verghese_lok_wen_alessandria_chen_kathariou_knabel_2011, title={comK prophage junction fragments as markers for listeria monocytogenes genotypes unique to individual meat and poultry processing plants and a model for rapid niche-specific adaptation, biofilm formation, and persistence}, volume={77}, DOI={10.1128/aem.00546-11}, abstractNote={ABSTRACT}, number={10}, journal={Applied and Environmental Microbiology}, author={Verghese, B. and Lok, M. and Wen, J. and Alessandria, V. and Chen, Y. and Kathariou, S. and Knabel, S.}, year={2011}, pages={3279–3292} }
 @article{yildirim_elhanafi_lin_hitchins_siletzky_kathariou_2010, title={Conservation of Genomic Localization and Sequence Content of Sau3AI-Like Restriction-Modification Gene Cassettes among Listeria monocytogenes Epidemic Clone I and Selected Strains of Serotype 1/2a}, volume={76}, ISSN={["1098-5336"]}, DOI={10.1128/aem.00648-10}, abstractNote={ABSTRACT}, number={16}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Yildirim, Suleyman and Elhanafi, Driss and Lin, Wen and Hitchins, Anthony D. and Siletzky, Robin M. and Kathariou, S.}, year={2010}, month={Aug}, pages={5577–5584} }
 @article{cheng_kim_lee_siletzky_kathariou_2010, title={DNA Probes for Unambiguous Identification of Listeria monocytogenes Epidemic Clone II Strains}, volume={76}, ISSN={["1098-5336"]}, DOI={10.1128/aem.03064-09}, abstractNote={ABSTRACT}, number={9}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Cheng, Ying and Kim, J. -W. and Lee, S. and Siletzky, R. M. and Kathariou, S.}, year={2010}, month={May}, pages={3061–3068} }
 @article{wright_wilson_miller_mandrell_siletzky_kathariou_2010, title={Differences in Methylation at GATC Sites in Genomic DNA of Campylobacter coli from Turkeys and Swine}, volume={76}, ISSN={["0099-2240"]}, DOI={10.1128/aem.00934-10}, abstractNote={ABSTRACT}, number={21}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Wright, Sandra and Wilson, Simone and Miller, William G. and Mandrell, Robert E. and Siletzky, Robin M. and Kathariou, Sophia}, year={2010}, month={Nov}, pages={7314–7317} }
 @article{mullapudi_siletzky_kathariou_2010, title={Diverse Cadmium Resistance Determinants in Listeria monocytogenes Isolates from the Turkey Processing Plant Environment}, volume={76}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01751-09}, abstractNote={ABSTRACT}, number={2}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Mullapudi, S. and Siletzky, R. M. and Kathariou, S.}, year={2010}, month={Jan}, pages={627–630} }
 @article{elhanafi_dutta_kathariou_2010, title={Genetic Characterization of Plasmid-Associated Benzalkonium Chloride Resistance Determinants in a Listeria monocytogenes Strain from the 1998-1999 Outbreak}, volume={76}, ISSN={["1098-5336"]}, DOI={10.1128/aem.02056-10}, abstractNote={ABSTRACT}, number={24}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Elhanafi, Driss and Dutta, Vikrant and Kathariou, Sophia}, year={2010}, month={Dec}, pages={8231–8238} }
 @article{azizoglu_kathariou_2010, title={Impact of Growth Temperature and Agar Versus Liquid Media on Freeze-Thaw Tolerance of Yersinia enterocolitica}, volume={7}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2009.0526}, abstractNote={Yersinia enterocolitica is a foodborne pathogen well known for its ability to grow at low temperatures. Recent studies with another psychrotrophic foodborne pathogen, Listeria monocytogenes, revealed that temperature of growth had pronounced impact on survival following repeated freezing and thawing (cryotolerance). Listerial cryotolerance was significantly more pronounced when bacteria were grown at 37 degrees C than following growth at either 4 degrees C or 25 degrees C. However, it is not known whether such impact of growth temperature is a general adaptation shared with other foodborne pathogens. In this study, we investigated the impact of growth temperature (4 degrees C, 25 degrees C, and 37 degrees C) on cryotolerance of Y. enterocolitica. In strong contrast to findings previously obtained with Listeria spp., cryotolerance of Y. enterocolitica was impaired following growth in liquid media at 37 degrees C, with cell concentration dropping to undetectable levels (<10(1) colony forming unit/mL) following as few as six freeze-thaw cycles. On the other hand, when the bacteria were grown at 4 degrees C, cryotolerance was significantly higher (p < 0.05), and substantial survival was maintained even after 18 cycles (2-5 log reduction, depending on strain). Enhanced cryotolerance was also observed with cultures grown at 25 degrees C. Bacteria grown at 37 degrees C on agar were significantly more cryotolerant than following growth at 37 degrees C in liquid media (p < 0.05). The data suggest species-specific impact of growth temperature and liquid versus agar medium on cryotolerance of cold-tolerant bacteria.}, number={9}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Azizoglu, Reha Onur and Kathariou, Sophia}, year={2010}, month={Sep}, pages={1125–1128} }
 @article{azizoglu_kathariou_2010, title={Inactivation of a Cold-Induced Putative RNA Helicase Gene of Listeria monocytogenes Is Accompanied by Failure To Grow at Low Temperatures but Does Not Affect Freeze-Thaw Tolerance}, volume={73}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028x-73.8.1474}, abstractNote={Freeze-thaw tolerance (cryotolerance) of Listeria monocytogenes is markedly influenced by temperature of growth of the bacteria, and may involve responses to low-temperature stresses encountered during freezing and thawing. A cold-sensitive mariner-based transposon mutant of L. monocytogenes F2365 was found to harbor a single insertion in LMOf2365_1746, encoding a putative RNA helicase, and earlier shown by other investigators to be induced during 4 degrees C growth of L. monocytogenes. The mutant had normal growth at 37 degrees C but completely failed to grow at either 4 or 10 degrees C, and had impaired growth and reduced swarming on soft agar at 25 degrees C. However, the mutation had no discernible influence on the ability of the bacteria to tolerate repeated freezing and thawing after growth at either 25 or 37 degrees C. The findings suggest that the transposon insertion in the putative helicase gene, in spite of the severely cold-sensitive phenotype that accompanies it, does not affect the ability of the bacteria to cope with cold-related stresses encountered during repeated freezing and thawing.}, number={8}, journal={JOURNAL OF FOOD PROTECTION}, author={Azizoglu, Reha O. and Kathariou, S.}, year={2010}, month={Aug}, pages={1474–1479} }
 @article{azizoglu_kathariou_2010, title={Temperature-Dependent Requirement for Catalase in Aerobic Growth of Listeria monocytogenes F2365}, volume={76}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01223-10}, abstractNote={ABSTRACT}, number={21}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Azizoglu, Reha Onur and Kathariou, Sophia}, year={2010}, month={Nov}, pages={6998–7003} }
 @article{gu_siletzky_wright_islam_kathariou_2009, title={Antimicrobial Susceptibility Profiles and Strain Type Diversity of Campylobacter jejuni Isolates from Turkeys in Eastern North Carolina}, volume={75}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.02012-08}, abstractNote={ABSTRACT}, number={2}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Gu, Weimin and Siletzky, Robin M. and Wright, Sandra and Islam, Mohammed and Kathariou, Sophia}, year={2009}, month={Jan}, pages={474–482} }
 @article{pan_breidt_kathariou_2009, title={Competition of Listeria monocytogenes serotype 1/2a and 4b strains in mixed-culture biofilms}, volume={75}, DOI={10.1128/AEM.00816-09}, abstractNote={ABSTRACT}, number={18}, journal={Applied and Environmental Microbiology}, author={Pan, Y. W. and Breidt, F. and Kathariou, S.}, year={2009}, pages={5846–5852} }
 @article{sperry_kathariou_edwards_wolf_2009, title={Multiple-Locus Variable-Number Tandem-Repeat Analysis as a Tool for Subtyping Listeria monocytogenes Strains (vol 46, pg 1435, 2008)}, volume={47}, ISSN={["0095-1137"]}, DOI={10.1128/jcm.00730-09}, number={6}, journal={JOURNAL OF CLINICAL MICROBIOLOGY}, author={Sperry, Katharine E. Volpe and Kathariou, Sophia and Edwards, Justin S. and Wolf, Leslie A.}, year={2009}, month={Jun}, pages={1984–1984} }
 @article{azizoglu_osborne_wilson_kathariou_2009, title={Role of Growth Temperature in Freeze-Thaw Tolerance of Listeria spp.}, volume={75}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.00458-09}, abstractNote={ABSTRACT}, number={16}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Azizoglu, Reha O. and Osborne, J. and Wilson, S. and Kathariou, S.}, year={2009}, month={Aug}, pages={5315–5320} }
 @article{kim_kathariou_2009, title={Temperature-Dependent Phage Resistance of Listeria monocytogenes Epidemic Clone II}, volume={75}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.02480-08}, abstractNote={ABSTRACT}, number={8}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Kim, Jae-Won and Kathariou, Sophia}, year={2009}, month={Apr}, pages={2433–2438} }
 @article{vishnivetskaya_kathariou_tiedje_2009, title={The Exiguobacterium genus: biodiversity and biogeography}, volume={13}, ISSN={["1433-4909"]}, DOI={10.1007/s00792-009-0243-5}, abstractNote={Bacteria of the genus Exiguobacterium are low G + C, Gram-positive facultative anaerobes that have been repeatedly isolated from ancient Siberian permafrost. In addition, Exiguobacterium spp. have been isolated from markedly diverse sources, including Greenland glacial ice, hot springs at Yellowstone National Park, the rhizosphere of plants, and the environment of food processing plants. Strains of this hereto little known bacterium that have been retrieved from such different (and often extreme) environments are worthy of attention as they are likely to be specifically adapted to such environments and to carry variations in the genome which may correspond to psychrophilic and thermophilic adaptations. However, comparative genomic investigations of Exiguobacterium spp. from different sources have been limited. In this study, we employed different molecular approaches for the comparative analysis of 24 isolates from markedly diverse environments including ancient Siberian permafrost and hot springs at Yellowstone National Park. Pulsed-field gel electrophoresis (PFGE) with I-CeuI (an intron-encoded endonuclease), AscI and NotI were optimized for the determination of genomic fingerprints of nuclease-producing isolates. The application of a DNA macroarray for 82 putative stress-response genes yielded strain-specific hybridization profiles. Cluster analyses of 16S rRNA gene sequence data, PFGE I-CeuI restriction patterns and hybridization profiles suggested that Exiguobacterium strains formed two distinct divisions that generally agreed with temperature ranges for growth. With few exceptions (e.g., Greenland ice isolate GIC31), psychrotrophic and thermophilic isolates belonged to different divisions.}, number={3}, journal={EXTREMOPHILES}, author={Vishnivetskaya, Tatiana A. and Kathariou, Sophia and Tiedje, James M.}, year={2009}, month={May}, pages={541–555} }
 @article{faith_kathariou_cheng_promadej_neudeck_zhang_luchansky_czuprynski_2009, title={The Role of L-monocytogenes Serotype 4b gtcA in Gastrointestinal Listeriosis in A/J Mice}, volume={6}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2008.0154}, abstractNote={Serotype 4b strains of Listeria monocytogenes have been responsible for most large outbreaks of listeriosis. In L. monocytogenes serotype 4b, gtcA and gltA have been implicated in serotype-specific glycosylation of the teichoic acid of the cell wall with galactose and glucose. In this study, we investigated the impact of mutations in gltA (resulting in absence of glucose on teichoic acid) and gtcA (resulting in absence of galactose, and markedly reduced glucose on teichoic acid) on virulence following intragastric infection of anesthetized A/J mice. The gltA mutant was not impaired in virulence in this model. In contrast, testing of gtcA mutants constructed in two different strains showed that the mutants were recovered in lower numbers than their respective parent strains from the spleen, liver, ceca, and gall bladders of intragastrically inoculated mice. Genetic complementation of the gtcA mutation partially restored gastrointestinal virulence. When mice were inoculated intravenously, the gtcA mutants were also recovered in lower numbers from the liver (for both mutant strains) and the spleen (for one mutant strain) than their respective parental strains. The mutants were also evaluated for invasion and intracellular multiplication in the Caco-2 human intestinal epithelial cell line. Inactivation of gltA did not affect invasion or intracellular growth of the bacteria. In contrast, gtcA mutants showed decreased invasion, but normal multiplication in Caco-2 cells. Overall, these data demonstrate a role for gtcA in the pathogenesis of gastrointestinal listeriosis in mice, and suggest that diminished ability of gtcA mutants to invade intestinal epithelial cells may be partly responsible for decreased gastrointestinal virulence.}, number={1}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Faith, Nancy and Kathariou, Sophia and Cheng, Ying and Promadej, Nattawan and Neudeck, Brien L. and Zhang, Qiuye and Luchansky, John and Czuprynski, Charles}, year={2009}, pages={39–48} }
 @article{kim_kim_kathariou_2008, title={Differential effects of temperature on natural transformation to erythromycin and nalidixic acid resistance in Campylobacter coli}, volume={74}, ISSN={["0099-2240"]}, DOI={10.1128/AEM.01075-08}, abstractNote={ABSTRACT}, number={19}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Kim, Joo-Sung and Kim, Jae-Won and Kathariou, S.}, year={2008}, month={Oct}, pages={6121–6125} }
 @article{chan_elhanafi_kathariou_2008, title={Genomic evidence for interspecies acquisition of chromosomal DNA from Campylobacter jejuni by Campylobacter coli strains of a turkey-associated clonal group (cluster II)}, volume={5}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2008.0113}, abstractNote={Previous multilocus sequence typing studies of Campylobacter coli from meat animals identified an unusual cluster of strains, primarily from turkeys, termed "cluster II" and characterized by the presence of the C. jejuni aspA103 allele. To characterize the extent of genomic input from C. jejuni in the aspA region of cluster II C. coli, we sequenced the 6.1 kb genomic region upstream of and including aspA from two turkey-derived cluster II strains (C. coli 6979 and C. coli 7474, of ST-1150 and ST-1161, respectively), as well as from a turkey-derived multidrug-resistant strain (C. coli 6818) representing a major sequence type (ST-1101) outside of cluster II. A gene encoding a putative CRP-family transcriptional regulator (CCO0137) was present in C. coli 6818 and the reference strain C. coli RM2228, whose genome has been sequenced, but not in either cluster II strain evaluated. This gene was also absent from C. jejuni NCTC 11168 and C. jejuni RM1221. Moreover, single nucleotide polymorphism (SNP) analysis revealed that in both cluster II strains, genes encoding subunit II of cytochrome d ubiquinol oxidase (cydB) and a putative aspartate racemase (Cj0085c) harbored numerous C. jejuni-specific SNPs. Interestingly, genes encoding subunit I of cytochrome d ubiquinol oxidase (cydA), uracil-DNA glycosylase (ung), and aspartate ammonia-lyase (aspA) harbored C. coli-specific SNPs in certain portions but C. jejuni-specific SNPs in others, suggesting that these were hybrid genes with C. jejuni-derived segments. Analysis of a ung mutant in C. coli 7474 indicated that the putative hybrid ung of this cluster II strain was functional. Our data suggest the occurrence of recombination events that resulted in genomic import of DNA from C. jejuni in the region between cydA and aspA in cluster II strains of C. coli.}, number={4}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Chan, Kamfai and Elhanafi, Driss and Kathariou, Sophia}, year={2008}, month={Aug}, pages={387–398} }
 @article{mullapudi_siletzky_kathariou_2008, title={Heavy-metal and benzalkonium chloride resistance of Listeria monocytogenes isolates from the environment of turkey-processing plants}, volume={74}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.02426-07}, abstractNote={ABSTRACT}, number={5}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Mullapudi, S. and Siletzky, R. M. and Kathariou, S.}, year={2008}, month={Mar}, pages={1464–1468} }
 @article{kim_siletzky_kathariou_2008, title={Host Ranges of Listeria-Specific Bacteriophages from the Turkey Processing Plant Environment in the United States}, volume={74}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01282-08}, abstractNote={ABSTRACT}, number={21}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Kim, Jae-Won and Siletzky, Robin M. and Kathariou, Sophia}, year={2008}, month={Nov}, pages={6623–6630} }
 @article{wright_carver_siletzky_romine_morrow_kathariou_2008, title={Longitudinal study of prevalence of Campylobacter jejuni and Campylobacter coli from turkeys and swine grown in close proximity}, volume={71}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028X-71.9.1791}, abstractNote={Eastern North Carolina is a major contributor to both turkey and swine production in the United States. In this region, turkeys and swine are frequently grown in close proximity and by common growers. To further characterize colonization of turkeys and swine with Campylobacter in such a setting, we investigated the prevalence of thermophilic campylobacters in eight paired operations involving turkey farms in close proximity to finishing swine farms. All 15 surveyed flocks and 15 herds were Campylobacter positive at one or more sampling times. Campylobacter was isolated from 1,310 (87%) of the 1,512 turkey samples and 1,116 (77%) of the 1,448 swine samples. Most (> 99%) campylobacters from swine samples were Campylobacter coli, found in 59 to 97% of the samples from the different herds. Both Campylobacterjejuni and C. coli were recovered from the turkey flocks (overall prevalences of 52 and 35%, respectively). Prevalence among flocks ranged from 31 to 86% for C. jejuni and 0 to 67% for C. coli, and both species were recovered from most flocks. Relative prevalence of C. coli was higher in young birds (brooders), whereas C. jejuni predominated in grow-out birds (P < 0.0001). The prevalence of C. coli in a swine herd was generally not a good predictor for prevalence of this species in the corresponding turkey flock. These findings indicate that even though turkeys and swine grown in proximity to each other were commonly colonized with thermophilic campylobacters, the relative prevalences of C. jejuni and C. coli appear to be host associated.}, number={9}, journal={JOURNAL OF FOOD PROTECTION}, author={Wright, S. L. and Carver, D. K. and Siletzky, R. M. and Romine, S. and Morrow, W. E. M. and Kathariou, S.}, year={2008}, month={Sep}, pages={1791–1796} }
 @article{sperry_kathariou_edwards_wolf_2008, title={Multiple-locus variable-number tandem-repeat analysis as a tool for subtyping Listeria monocytogenes strains}, volume={46}, ISSN={["1098-660X"]}, DOI={10.1128/JCM.02207-07}, abstractNote={ABSTRACT}, number={4}, journal={JOURNAL OF CLINICAL MICROBIOLOGY}, author={Sperry, Katharine E. Volpe and Kathariou, Sophia and Edwards, Justin S. and Wolf, Leslie A.}, year={2008}, month={Apr}, pages={1435–1450} }
 @article{cheng_promadej_kim_kathariou_2008, title={Teichoic acid glycosylation mediated by gtcA is required for phage adsorption and susceptibility of Listeria monocytogenes serotype 4b}, volume={74}, ISSN={["0099-2240"]}, DOI={10.1128/AEM.01773-07}, abstractNote={ABSTRACT}, number={5}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Cheng, Ying and Promadej, Nattawan and Kim, Jae-Won and Kathariou, S.}, year={2008}, month={Mar}, pages={1653–1655} }
 @article{faith_kathariou_neudeck_luchansky_czuprynski_2007, title={A P60 mutant of Listeria monocytogenes is impaired in its ability to cause infection in intragastrically inoculated mice}, volume={42}, ISSN={["0882-4010"]}, DOI={10.1016/j.micpath.2007.01.004}, abstractNote={A spontaneous P60 mutant of Listeria monocytogenes was less able to cause systemic infection in A/J mice, following intragastric inoculation, than the parental wild type strain (SLCC 5764, serotype 1/2a). Significantly fewer CFU were recovered from internal organs (spleen, liver, gall bladder) and from the cecum of mice inoculated intragastrically with the P60 mutant than mice inoculated with wild type L. monocytogenes. The P60 mutant also exhibited a diminished ability to invade and multiply within Caco-2 intestinal epithelial cells. These findings indicate that P60 is required for maximal virulence of L. monocytogenes in the gastrointestinal tract of mice.}, number={5-6}, journal={MICROBIAL PATHOGENESIS}, author={Faith, Nancy G. and Kathariou, Sophia and Neudeck, Brien L. and Luchansky, John B. and Czuprynski, Charles J.}, year={2007}, pages={237–241} }
 @article{cheng_yue_elhanafi_kathariou_2007, title={Absence of serotype-specific surface antigen in laboratory variants of epidemic-associated Listeria monocytogenes strains}, volume={73}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.00473-07}, abstractNote={ABSTRACT}, number={19}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Cheng, Ying and Yue, Lili and Elhanafi, Driss and Kathariou, S.}, year={2007}, month={Oct}, pages={6313–6316} }
 @article{d'lima_miller_mandrell_wright_siletzky_carver_kathariou_2007, title={Clonal population structure and specific genotypes of multidrug-resistant Campylobacter coli from turkeys}, volume={73}, ISSN={["0099-2240"]}, DOI={10.1128/AEM.02346-06}, abstractNote={ABSTRACT}, number={7}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={D'lima, C. B. and Miller, W. G. and Mandrell, R. E. and Wright, S. L. and Siletzky, R. M. and Carver, D. K. and Kathariou, S.}, year={2007}, month={Apr}, pages={2156–2164} }
 @article{vishnivetskaya_siletzky_jefferies_tiedje_kathariou_2007, title={Effect of low temperature and culture media on the growth and freeze-thawing tolerance of Exiguobacterium strains}, volume={54}, ISSN={["0011-2240"]}, DOI={10.1016/j.cryobiol.2007.01.008}, abstractNote={Bacteria of the genus Exiguobacterium have been repeatedly isolated from ancient permafrost sediments of the Kolyma lowland of Northeast Eurasia. Here we report that the Siberian permafrost isolates Exiguobacterium sibiricum 255-15, E. sibiricum 7-3, Exiguobacterium undae 190-11 and E. sp. 5138, as well as Exiguobacterium antarcticum DSM 14480, isolated from a microbial mat sample of Lake Fryxell (McMurdo Dry Valleys, Antarctica), were able to grow at temperatures ranging from −6 to 40 °C. In comparison to cells grown at 24 °C, the cold-grown cells of these strains tended to be longer and wider. We also investigated the effect of growth conditions (broth or surface growth, and temperature) on cryotolerance of the Exiguobacterium strains. Bacteria grown in broth at 4 °C showed markedly greater survival following freeze-thawing treatments (20 repeated cycles) than bacteria grown in broth at 24 °C. Surprisingly, significant protection to repeated freeze-thawing was also observed when bacteria were grown on agar at either 4 or 24 °C.}, number={2}, journal={CRYOBIOLOGY}, author={Vishnivetskaya, Tatiana A. and Siletzky, Robin and Jefferies, Natalie and Tiedje, James M. and Kathariou, Sophia}, year={2007}, month={Apr}, pages={234–240} }
 @article{bazaco_eifert_williams_kathariou_2007, title={Quantitative recovery of Listeria monocytogenes and select Salmonella serotypes from environmental sample media}, volume={90}, number={1}, journal={Journal of AOAC International}, author={Bazaco, M. C. and Eifert, J. D. and Williams, R. C. and Kathariou, S.}, year={2007}, pages={250–257} }
 @article{chan_miller_mandrell_kathariou_2007, title={The absence of intervening sequences in 23S rRNA genes of Campylobacter coli isolates from turkeys is a unique attribute of a cluster of related strains which also lack resistance to erythromycin}, volume={73}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01995-06}, abstractNote={ABSTRACT}, number={4}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Chan, Kamfai and Miller, William G. and Mandrell, Robert E. and Kathariou, Sophia}, year={2007}, month={Feb}, pages={1208–1214} }
 @article{gharst_hanson_kathariou_2006, title={Effect of direct culture versus selective enrichment on the isolation of thermophilic Campylobacter from feces of mature cattle at harvest}, volume={69}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028X-69.5.1024}, abstractNote={Campylobacterjejuni and Campylobacter coli are leading bacterial causes of human gastroenteritis in the United States and other industrialized nations. These organisms frequently colonize avian hosts, including commercial poultry, but are also found in the gastrointestinal tract of other warm-blooded animals, including swine, sheep, and cattle. This study investigated the effect of direct culture versus selective enrichment on the isolation of thermophilic Campylobacter from the colon of 610 cattle. Fecal samples were taken from the colon of mature cattle (older than 30 months of age) immediately after slaughter in a commercial abattoir over a period of 17 months. Campylobacter was isolated from 23.4% of the animals. Most (93%) of the culture-confirmed Campylobacter isolates were C. jejuni, with the remaining 7% being C. coli. Additionally, of the 143 samples from which pure cultures of Campylobacter could be isolated, 72 (50.3%) were positive only with selective enrichment, 18 (12.6%) were positive only with direct plating, and 53 (37.1%) were positive by both methods. The data suggest that, even though selective enrichment was more effective than direct plating, both direct plating and selective enrichment protocols might need to be employed for optimal surveillance of C. jejuni in fecal material from cattle.}, number={5}, journal={JOURNAL OF FOOD PROTECTION}, author={Gharst, G and Hanson, D and Kathariou, S}, year={2006}, month={May}, pages={1024–1027} }
 @article{miller_englen_kathariou_wesley_wang_pittenger-alley_siletz_muraoka_fedorka-cray_mandrell_2006, title={Identification of host-associated alleles by multilocus sequence typing of Campylobacter coli strains from food animals}, volume={152}, ISSN={1350-0872 1465-2080}, url={http://dx.doi.org/10.1099/mic.0.28348-0}, DOI={10.1099/mic.0.28348-0}, abstractNote={
                  Campylobacter coli is a food-borne pathogen associated increasingly with human gastroenteritis. C. coli has a high prevalence in swine, but is isolated also from cattle and poultry. Multilocus sequence typing (MLST) systems have been developed to differentiate C. coli strains. Although substantial allelic diversity was identified across all seven C. coli MLST loci, no correlations were made in two previous studies between allele or sequence type (ST) and the source of the organism. However, this may be due to either the relatively small number or the low diversity of C. coli strains used to validate both MLST studies. This study describes the typing of 488 C. coli strains from 4 different food animal sources (cattle, chickens, swine and turkeys), collected at different times over a 6 year period from different USA geographical locations. A total of 149 STs were identified. The 185 swine strains were the most diverse, possessing 82 STs. The cattle strains were the most clonal; 52/63 (83 %) strains possessed a single ST (ST-1068). A subpopulation of C. coli strains, collected primarily from turkeys, was identified, containing both C. coli- and Campylobacter jejuni-associated MLST alleles, specifically the C. jejuni allele aspA103. The majority of STs and alleles were host associated, i.e. found primarily in strains from a single food-animal source. Only 12/149 (8 %) STs were found in multiple sources. Additionally, the majority (34/46, 74 %) of major (n>5) alleles were more prevalent in certain hosts (swine, poultry). The presence of host-associated C. coli MLST alleles could lead potentially to more efficient source tracking in this species, especially in the trace-back of both sporadic and outbreak human clinical C. coli strains to animal sources.}, number={1}, journal={Microbiology}, publisher={Microbiology Society}, author={Miller, M.A. and Englen, M.D. and Kathariou, S. and Wesley, I. and Wang, Guilin and Pittenger-Alley, Lauren and Siletz, Robin M. and Muraoka, Wayne and Fedorka-Cray, P.J. and Mandrell, R.E.}, year={2006}, month={Jan}, pages={245–255} }
 @article{kim_carver_kathariou_2006, title={Natural transformation-mediated transfer of erythromycin resistance in Campylobacter coli strains from turkeys and swine}, volume={72}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.72.2.1316-1321.2006}, abstractNote={ABSTRACT}, number={2}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Kim, JS and Carver, DK and Kathariou, S}, year={2006}, month={Feb}, pages={1316–1321} }
 @article{qiu_kathariou_lubman_2006, title={Proteomic analysis of cold adaptation in a Siberian permafrost bacterium - Exiguobacterium sibiricum 255-15 by two-dimensional liquid separation coupled with mass spectrometry}, volume={6}, ISSN={["1615-9853"]}, DOI={10.1002/pmic.200600071}, abstractNote={Abstract}, number={19}, journal={PROTEOMICS}, author={Qiu, Yinghua and Kathariou, Sophia and Lubman, David M.}, year={2006}, month={Oct}, pages={5221–5233} }
 @article{pan_breidt_kathariou_2006, title={Resistance of Listeria monocytogenes biofilms to sanitizing agents in a simulated food processing environment}, volume={72}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01065-06}, abstractNote={ABSTRACT}, number={12}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Pan, Y. and Breidt, F., Jr. and Kathariou, S.}, year={2006}, month={Dec}, pages={7711–7717} }
 @article{reina_breidt_fleming_kathariou_2005, title={Isolation and selection of lactic acid bacteria as biocontrol agents for nonacidified, refrigerated pickles}, volume={70}, ISSN={["1750-3841"]}, DOI={10.1111/j.1365-2621.2005.tb09050.x}, abstractNote={AB isolates w AB isolates w AB isolates w AB isolates were obtained. Among the L e obtained. Among the L e obtained. Among the L e obtained. Among the L e obtained. Among the LAB identified w AB identified w AB identified w}, number={1}, journal={JOURNAL OF FOOD SCIENCE}, author={Reina, LD and Breidt, F and Fleming, HP and Kathariou, S}, year={2005}, pages={M7–M11} }
 @article{eifert_curtis_bazaco_meinersmann_berrang_kernodle_stam_jaykus_kathariou_2005, title={Molecular characterization of Listeria monocytogenes of the serotype 4b complex (4b, 4d, 4e) from two turkey processing plants}, volume={2}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2005.2.192}, abstractNote={Most foodborne outbreaks of listeriosis have been found to involve a small number of closely related strains of Listeria monocytogenes serotype 4b. The ecology of these organisms and their reservoirs in nature or in the processing plant environment, however, remain poorly understood. Surveys of environmental samples from two turkey processing plants in the United States indicated presence of L. monocytogenes of the serotype 4b complex (serotype 4b and the closely related serotypes 4d and 4e). In addition, environmental and raw product samples from one plant repeatedly yielded isolates with genetic markers typical of two major serotype 4b epidemic clonal groups, ECI and ECII. The pulsed field gel electrophoresis (PFGE) profiles of these isolates, however, were clearly distinct from those of confirmed epidemic-associated strains. Furthermore, we observed minor but consistent differences in PFGE profiles of isolates that harbored ECI- or ECII-specific genetic markers, and that were obtained at different sampling times from the same plant. The findings suggest processing plant persistence (or repeated introductions) and genomic diversification of L. monocytogenes serotype 4b isolates that harbor ECI- or ECII-specific genetic markers. Such diversification would need to be taken into consideration in further efforts to elucidate the evolution and epidemiology of these organisms.}, number={3}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Eifert, J. D. and Curtis, P. A. and Bazaco, M. C. and Meinersmann, R. J. and Berrang, M. E. and Kernodle, S. and Stam, C. and Jaykus, L. -A. and Kathariou, S.}, year={2005}, pages={192–200} }
 @article{vishnivetskaya_kathariou_2005, title={Putative transposases conserved in Exiguobacterium isolates from ancient Siberian permafrost and from contemporary surface habitats}, volume={71}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.71.11.6954-6962.2005}, abstractNote={ABSTRACT}, number={11}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Vishnivetskaya, TA and Kathariou, S}, year={2005}, month={Nov}, pages={6954–6962} }
 @article{lee_reimers_barnes_d'lima_carver_kathariou_2005, title={Strain persistence and fluctuation of multiple-antibiotic resistant Campylobacter coli colonizing turkeys over successive production cycles}, volume={2}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2005.2.103}, abstractNote={The dynamics of colonization of turkeys by thermophilic campylobacters that are resistant to multiple antibiotics is poorly understood. In this study, we monitored cecal colonization of turkeys by Campylobacter over three successive production cycles at the same farm. Campylobacter isolated from the ceca was predominantly C. coli in all three flocks. Isolates with two distinct fla types that represented a single clonal group based on pulsed-field gel electrophoresis and that were resistant to multiple antibiotics (tetracycline, streptomycin, ampicillin, erythromycin, kanamycin, nalidixic acid, and ciprofloxacin) predominated throughout the three production cycles. The relative prevalence of each fla type, however, varied significantly from one flock to the next. The repeated isolation of these multiresistant C. coli from successive flocks likely reflected persistence of the organisms in currently unknown reservoirs in the production environment or, alternatively, repeated introduction events followed by establishment of these bacteria in each successive flock.}, number={1}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Lee, Bong Choon and Reimers, Nancy and Barnes, H. John and D'Lima, Carol and Carver, Donna and Kathariou, Sophia}, year={2005}, pages={103–110} }
 @article{smith_reimers_barnes_lee_siletzky_kathariou_2004, title={Campylobacter colonization of sibling turkey flocks reared under different management conditions}, volume={67}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028X-67.7.1463}, abstractNote={Uncertainty exists concerning the key factors contributing to Campylobacter colonization of poultry, especially the possible role of vertical transmission from breeder hens to young birds. A longitudinal study of Campylobacter colonization was performed in two sibling pairs of turkey flocks (four flocks total). Each pair of sibling flocks shared breeder hen populations and was obtained from the same hatchery. One flock of each pair was grown on a commercial farm, and the other was grown in an instructional demonstration unit (Teaching Animal Unit [TAU]). Flocks were located within a 60-mi (96.8-km) radius. The time of placement, feed formulations, stocking density, and general husbandry were the same for both flocks, and each flock was processed at a commercial processing plant following standard feed withdrawal and transport protocols. Both flocks grown on the commercial farms became colonized with Campylobacter between weeks 2 and 3 and remained colonized until processing. Between 80 and 90% of isolates were Campylobacter coli, and the remainder were Campylobacter jejuni. In contrast, neither C. coli nor C. jejuni were isolated from either of the TAU flocks at any time during the production cycle. None of the fla types of Campylobacter from the breeders that provided poults to one of the commercial flocks matched those from the progeny. These results failed to provide evidence for vertical transmission and indicate that this type of transmission either did not occur or was not sufficient to render the TAU turkey flocks Campylobacter positive. Management practices such as proper litter maintenance, controlled traffic between the TAU farm and other turkey flocks, and other less well-defined aspects of turkey production were likely responsible for the absence of Campylobacter in the TAU flocks before harvest.}, number={7}, journal={JOURNAL OF FOOD PROTECTION}, author={Smith, K and Reimers, N and Barnes, HJ and Lee, BC and Siletzky, R and Kathariou, S}, year={2004}, month={Jul}, pages={1463–1468} }
 @misc{keener_bashor_curtis_sheldon_kathariou_2004, title={Comprehensive review of Campylobacter and poultry processing}, volume={3}, ISSN={["1541-4337"]}, DOI={10.1111/j.1541-4337.2004.tb00060.x}, abstractNote={ABSTRACT}, number={2}, journal={COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY}, author={Keener, KM and Bashor, MP and Curtis, PA and Sheldon, BW and Kathariou, S}, year={2004}, month={Apr}, pages={105–116} }
 @article{bashor_curtis_keener_sheldon_kathariou_osborne_2004, title={Effects of carcass washers on Campylobacter contamination in large broiler processing plants}, volume={83}, ISSN={["1525-3171"]}, DOI={10.1093/ps/83.7.1232}, abstractNote={Campylobacter, a major foodborne pathogen found in poultry products, remains a serious problem facing poultry processors. Campylobacter research has primarily focused on detection methods, prevalence, and detection on carcasses; limited research has been conducted on intervention. The aim of this study was to assess the effectiveness of carcass washing systems in 4 large broiler-processing plants in removing Campylobacter species. Washing systems evaluated included combinations of inside/outside carcass washers and homemade cabinet washers. Processing aids evaluated were trisodium phosphate (TSP) and acidified sodium chlorite (ASC). The washer systems consisted of 1 to 3 carcass washers and used from 2.16 to 9.73 L of water per carcass. The washer systems used chlorinated water with 25 to 35 ppm of total chlorine. These washer systems on average reduced Campylobacter populations by log 0.5 cfu/mL from log 4.8 cfu/mL to log 4.3 cfu/mL. Washer systems with TSP or ASC reduced Campylobacter populations on average by an additional log 1.03 to log 1.26, respectively. Total average reductions in Campylobacter populations across the washer system and chill tank were log 0.76 cfu/mL. Washer systems that included antimicrobial systems had total average reductions in Campylobacter populations of log 1.53 cfu/mL. These results suggest that carcass washer systems consisting of multiple washers provide minimal reductions in Campylobacter populations found on poultry in processing plants. A more effective treatment of reducing Campylobacter populations is ASC or TSP treatment; however, these reductions, although significant, will not eliminate the organism from raw poultry.}, number={7}, journal={POULTRY SCIENCE}, author={Bashor, MP and Curtis, PA and Keener, KM and Sheldon, BW and Kathariou, S and Osborne, JA}, year={2004}, month={Jul}, pages={1232–1239} }
 @article{yildirim_lin_hitchins_jaykus_altermann_klaenhammer_kathariou_2004, title={Epidemic clone I-specific genetic markers in strains of Listeria monocytogenes serotype 4b from foods}, volume={70}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.70.7.4158-4164.2004}, abstractNote={ABSTRACT}, number={7}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Yildirim, S and Lin, W and Hitchins, AD and Jaykus, LA and Altermann, E and Klaenhammer, TR and Kathariou, S}, year={2004}, month={Jul}, pages={4158–4164} }
 @article{yildirim_lin_hitchins_jaykus_altermann_klaenhammer_kathariou_2004, title={Epidemic clone I-specific genetic markers in strains of Listeria monocytogenes serotype 4b from foods (vol 70, pg 4158, 2004)}, volume={70}, ISSN={["0099-2240"]}, DOI={10.1128/aem.70.12.7581.2004}, abstractNote={Listeria monocytogenes contamination of ready-to-eat foods has been implicated in numerous outbreaks of food-borne listeriosis. However, the health hazards posed by L. monocytogenes detected in foods may vary, and speculations exist that strains actually implicated in illness may constitute only a fraction of those that contaminate foods. In this study, examination of 34 serogroup 4 (putative or confirmed serotype 4b) isolates of L. monocytogenes obtained from various foods and food-processing environments, without known implication in illness, revealed that many of these strains had methylation of cytosines at GATC sites in the genome, rendering their DNA resistant to digestion by the restriction endonuclease Sau3AI. These strains also harbored a gene cassette with putative restriction-modification system genes as well as other, genomically unlinked genetic markers characteristic of the major epidemic-associated lineage of L. monocytogenes (epidemic clone I), implicated in numerous outbreaks in Europe and North America. This may reflect a relatively high fitness of strains with these genetic markers in foods and food-related environments relative to other serotype 4b strains and may partially account for the repeated involvement of such strains in human food-borne listeriosis. Food contamination by Listeria monocytogenes has been implicated in numerous outbreaks and sporadic cases of human illness. Most commonly implicated in listeriosis are highly processed, ready-to-eat (RTE) foods that are kept refrigerated for various periods of time. At risk for listeriosis are people in the extremes of age, pregnant women and their fetuses, cancer patients, and others experiencing immunosuppression (13, 24, 35, 38). Listeriosis can have severe symptoms (septicemia, meningitis, and stillbirths) and a high mortality rate (20 to 30%). Hence, regulations exist in numerous nations concerning the density (e.g., 1 CFU/25 g) of cells of the etiologic agent permissible in RTE foods. Such regulations are based on the hypothesis that any L. monocytogenes strain that can be detected in RTE foods has the potential to pose serious hazards to human health. The potential hazard posed by listerial contamination of RTE foods can be influenced by the number of cells at the point of consumption, which would depend on conditions of storage, type of food matrix and its impact on growth, presence of competing microflora and antimicrobial agents, etc. In addition, the strain type of L. monocytogenes involved may be of importance. It is likely, based on studies with other bacterial pathogens, that some strains and strain clusters (clonal groups) within the species might be more pathogenic than others. Speculations have been formulated that only a fraction of the strains of L. monocytogenes found in foods may be capable of causing human illness (20). There is indeed evidence that the repertoire of strains ca}, number={12}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Yildirim, S and Lin, W and Hitchins, AD and Jaykus, LA and Altermann, E and Klaenhammer, TR and Kathariou, S}, year={2004}, month={Dec}, pages={7581–7581} }
 @article{evans_swaminathan_graves_altermann_klaenhammer_fink_kernodle_kathariou_2004, title={Genetic markers unique to Listeria monocytogenes serotype 4b differentiate epidemic clone II (hot dog outbreak strains) from other lineages}, volume={70}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.70.4.2383-2390.2004}, abstractNote={ABSTRACT}, number={4}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Evans, MR and Swaminathan, B and Graves, LM and Altermann, E and Klaenhammer, TR and Fink, RC and Kernodle, S and Kathariou, S}, year={2004}, month={Apr}, pages={2383–2390} }
 @article{johnson_jinneman_stelma_smith_lye_messer_ulaszek_evsen_gendel_bennett_et al._2004, title={Natural atypical Listeria innocua strains with Listeria monocytogenes pathogenicity island 1 genes}, volume={70}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.70.7.4256-4266.2004}, abstractNote={ABSTRACT}, number={7}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Johnson, J and Jinneman, K and Stelma, G and Smith, BG and Lye, D and Messer, J and Ulaszek, J and Evsen, L and Gendel, S and Bennett, RW and et al.}, year={2004}, month={Jul}, pages={4256–4266} }
 @article{nelson_fouts_mongodin_ravel_deboy_kolonay_rasko_angiuoli_gill_paulsen_et al._2004, title={Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species}, volume={32}, ISSN={["0305-1048"]}, DOI={10.1093/nar/gkh562}, abstractNote={The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69 strain-specific genes were identified in L.monocytogenes strains F2365 (serotype 4b, cheese isolate), F6854 (serotype 1/2a, frankfurter isolate) and H7858 (serotype 4b, meat isolate), respectively. Eighty-three genes were restricted to serotype 1/2a and 51 to serotype 4b strains. These strain- and serotype-specific genes probably contribute to observed differences in pathogenicity, and the ability of the organisms to survive and grow in their respective environmental niches. The serotype 1/2a-specific genes include an operon that encodes the rhamnose biosynthetic pathway that is associated with teichoic acid biosynthesis, as well as operons for five glycosyl transferases and an adenine-specific DNA methyltransferase. A total of 8603 and 105 050 high quality single nucleotide polymorphisms (SNPs) were found on the draft genome sequences of strain H7858 and strain F6854, respectively, when compared with strain F2365. Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs.}, number={8}, journal={NUCLEIC ACIDS RESEARCH}, author={Nelson, KE and Fouts, DE and Mongodin, EF and Ravel, J and DeBoy, RT and Kolonay, JF and Rasko, DA and Angiuoli, SV and Gill, SR and Paulsen, IT and et al.}, year={2004}, month={Apr}, pages={2386–2395} }
 @article{li_kathariou_2003, title={An improved cloning vector for construction of gene replacements in Listeria monocytogenes}, volume={69}, DOI={10.1128/AEM.69.5.3020-3023.2003}, abstractNote={ABSTRACT}, number={5}, journal={Applied and Environmental Microbiology}, author={Li, G. J. and Kathariou, S.}, year={2003}, pages={3020–3023} }
 @misc{kathariou_2002, title={Listeria monocytogenes virulence and pathogenicity, a food safety perspective}, volume={65}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028X-65.11.1811}, abstractNote={Several virulence factors of Listeria monocytogenes have been identified and extensively characterized at the molecular and cell biologic levels, including the hemolysin (listeriolysin O), two distinct phospholipases, a protein (ActA), several internalins, and others. Their study has yielded an impressive amount of information on the mechanisms employed by this facultative intracellular pathogen to interact with mammalian host cells, escape the host cell's killing mechanisms, and spread from one infected cell to others. In addition, several molecular subtyping tools have been developed to facilitate the detection of different strain types and lineages of the pathogen, including those implicated in common-source outbreaks of the disease. Despite these spectacular gains in knowledge, the virulence of L. monocytogenes as a foodborne pathogen remains poorly understood. The available pathogenesis and subtyping data generally fail to provide adequate insight about the virulence of field isolates and the likelihood that a given strain will cause illness. Possible mechanisms for the apparent prevalence of three serotypes (1/2a, 1/2b, and 4b) in human foodborne illness remain unidentified. The propensity of certain strain lineages (epidemic clones) to be implicated in common-source outbreaks and the prevalence of serotype 4b among epidemic-associated stains also remain poorly understood. This review first discusses current progress in understanding the general features of virulence and pathogenesis of L. monocytogenes. Emphasis is then placed on areas of special relevance to the organism's involvement in human foodborne illness, including (i) the relative prevalence of different serotypes and serotype-specific features and genetic markers; (ii) the ability of the organism to respond to environmental stresses of relevance to the food industry (cold, salt, iron depletion, and acid); (iii) the specific features of the major known epidemic-associated lineages; and (iv) the possible reservoirs of the organism in animals and the environment and the pronounced impact of environmental contamination in the food processing facilities. Finally, a discussion is provided on the perceived areas of special need for future research of relevance to food safety, including (i) theoretical modeling studies of niche complexity and contamination in the food processing facilities; (ii) strain databases for comprehensive molecular typing; and (iii) contributions from genomic and proteomic tools, including DNA microarrays for genotyping and expression signatures. Virulence-related genomic and proteomic signatures are expected to emerge from analysis of the genomes at the global level, with the support of adequate epidemiologic data and access to relevant strains.}, number={11}, journal={JOURNAL OF FOOD PROTECTION}, author={Kathariou, S}, year={2002}, month={Nov}, pages={1811–1829} }
 @article{tran_kathariou_2002, title={Restriction fragment length polymorphisms detected with novel DNA probes differentiate among diverse lineages of serogroup 4 Listeria monocytogenes and identify four distinct lineages in serotype 4b}, volume={68}, ISSN={["0099-2240"]}, DOI={10.1128/AEM.68.1.59-64.2002}, abstractNote={ABSTRACT}, number={1}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Tran, HL and Kathariou, S}, year={2002}, month={Jan}, pages={59–64} }
 @article{lei_fiedler_lan_kathariou_2001, title={A novel serotype-specific gene cassette (gltA-gltB) is required for expression of teichoic acid-associated surface antigens in Listeria monocytogenes of serotype 4b}, volume={183}, ISSN={["0021-9193"]}, DOI={10.1128/jb.183.4.1133-1139.2001}, abstractNote={ABSTRACT}, number={4}, journal={JOURNAL OF BACTERIOLOGY}, author={Lei, XH and Fiedler, F and Lan, Z and Kathariou, S}, year={2001}, month={Feb}, pages={1133–1139} }
 @article{chan_tran_kanenaka_kathariou_2001, title={Survival of clinical and poultry-derived isolates of Campylobacter jejuni at a low temperature (4 degrees C)}, volume={67}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.67.9.4186-4191.2001}, abstractNote={ABSTRACT}, number={9}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Chan, KF and Tran, HL and Kanenaka, RY and Kathariou, S}, year={2001}, month={Sep}, pages={4186–4191} }
 @article{lan_fiedler_kathariou_2000, title={A sheep in wolf's clothing: Listeria innocua strains with teichoic acid-associated surface antigens and genes characteristic of Listeria monocytogenes serogroup 4}, volume={182}, ISSN={["0021-9193"]}, DOI={10.1128/JB.182.21.6161-6168.2000}, abstractNote={ABSTRACT}, number={21}, journal={JOURNAL OF BACTERIOLOGY}, author={Lan, Z and Fiedler, F and Kathariou, S}, year={2000}, month={Nov}, pages={6161–6168} }